1
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Edri R, Williams LD, Frenkel-Pinter M. From Catalysis of Evolution to Evolution of Catalysis. Acc Chem Res 2024. [PMID: 39373892 DOI: 10.1021/acs.accounts.4c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
ConspectusThe mystery of the origins of life is one of the most difficult yet intriguing challenges to which humanity has grappled. How did biopolymers emerge in the absence of enzymes (evolved biocatalysts), and how did long-lasting chemical evolution find a path to the highly selective complex biology that we observe today? In this paper, we discuss a chemical framework that explores the very roots of catalysis, demonstrating how standard catalytic activity based on chemical and physical principles can evolve into complex machineries. We provide several examples of how prebiotic catalysis by small molecules can be exploited to facilitate polymerization, which in biology has transformed the nature of catalysis. Thus, catalysis evolved, and evolution was catalyzed, during the transformation of prebiotic chemistry to biochemistry. Traditionally, a catalyst is defined as a substance that (i) speeds up a chemical reaction by lowering activation energy through different chemical mechanisms and (ii) is not consumed during the course of the reaction. However, considering prebiotic chemistry, which involved a highly diverse chemical space (i.e., high number of potential reactants and products) and constantly changing environment that lacked highly sophisticated catalytic machinery, we stress here that a more primitive, broader definition should be considered. Here, we consider a catalyst as any chemical species that lowers activation energy. We further discuss various demonstrations of how simple prebiotic molecules such as hydroxy acids and mercaptoacids promote the formation of peptide bonds via energetically favored exchange reactions. Even though the small molecules are partially regenerated and partially retained within the resulting oligomers, these prebiotic catalysts fulfill their primary role. Catalysis by metal ions and in complex chemical mixtures is also highlighted. We underline how chemical evolution is primarily dictated by kinetics rather than thermodynamics and demonstrate a novel concept to support this notion. Moreover, we propose a new perspective on the role of water in prebiotic catalysis. The role of water as simply a "medium" obscures its importance as an active participant in the chemistry of life, specifically as a very efficient catalyst and as a participant in many chemical transformations. Here we highlight the unusual contribution of water to increasing complexification over the course of chemical evolution. We discuss possible pathways by which prebiotic catalysis promoted chemical selection and complexification. Taken together, this Account draws a connection line between prebiotic catalysis and contemporary biocatalysis and demonstrates that the fundamental elements of chemical catalysis are embedded within today's biocatalysts. This Account illustrates how the evolution of catalysis was intertwined with chemical evolution from the very beginning.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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2
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Kuroiwa K, Matsumura Y, Nagano K, Kishimoto R, Yoshizawa M, Fujimura A, Shimaki N, Sakuragi M, Oda-Ueda N. Supramolecular Hybrids of Proteins from Habu Snake Venom with Discrete [Pt(CN) 4] 2- Complex. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39267606 DOI: 10.1021/acsami.4c09837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
The venom of the Habu snake Protobothrops flavoviridis (P. flavoviridis) is known to contain a diverse array of proteins and peptides, with a notable presence of phospholipase A2 (PLA2) enzymes. These PLA2 enzymes have been extensively studied for their function and molecular evolution. Nevertheless, several aspects, such as the physical properties and the self-assembly mechanism of hierarchical structure from the nanoscale to the microscale with different chemical compounds, remain poorly understood. This study aims to fill this knowledge gap by investigating the behavior of enzyme components purified from P. flavoviridis venom in the presence of anionic [Pt(CN)4]2- complexes, which have the potential for soft metallophilic interactions and interesting optical properties. The purified PLA2 isozymes were diluted in Dulbecco's phosphate buffered saline (D-PBS (-)) and combined with the anionic metal complex, resulting in the formation of microstructures several micrometers in size, which further grew to form fibrous structures. This novel approach of combining PLA2 enzymes with discrete functional metal complexes opens up exciting possibilities for designing flexible and functional supramolecular and biomolecular hybrid systems in aqueous environments. These findings shed light on the potential applications of snake venom enzymes in nanotechnology and bioengineering.
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Affiliation(s)
- Keita Kuroiwa
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Yusei Matsumura
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Keito Nagano
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Reina Kishimoto
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Mai Yoshizawa
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Aoi Fujimura
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Nobuhito Shimaki
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Mina Sakuragi
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Naoko Oda-Ueda
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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3
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Erckert K, Rost B. Assessing the role of evolutionary information for enhancing protein language model embeddings. Sci Rep 2024; 14:20692. [PMID: 39237735 PMCID: PMC11377704 DOI: 10.1038/s41598-024-71783-8] [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: 05/14/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024] Open
Abstract
Embeddings from protein Language Models (pLMs) are replacing evolutionary information from multiple sequence alignments (MSAs) as the most successful input for protein prediction. Is this because embeddings capture evolutionary information? We tested various approaches to explicitly incorporate evolutionary information into embeddings on various protein prediction tasks. While older pLMs (SeqVec, ProtBert) significantly improved through MSAs, the more recent pLM ProtT5 did not benefit. For most tasks, pLM-based outperformed MSA-based methods, and the combination of both even decreased performance for some (intrinsic disorder). We highlight the effectiveness of pLM-based methods and find limited benefits from integrating MSAs.
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Affiliation(s)
- Kyra Erckert
- TUM School of Computation, Information and Technology, Bioinformatics & Computational Biology - i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany.
- TUM Graduate School, Center of Doctoral Studies in Informatics and Its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany.
| | - Burkhard Rost
- TUM School of Computation, Information and Technology, Bioinformatics & Computational Biology - i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching/Munich, Germany
- TUM School of Life Sciences Weihenstephan (TUM-WZW), Alte Akademie 8, Freising, Germany
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4
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Wang J, Chao B, Piesner J, Kelly F, Petrie SK, Xiao X, Li BX. CG-SLENP: A Chemical Genetics Strategy To Selectively Label Existing Proteins and Newly Synthesized Proteins. JACS AU 2024; 4:3146-3156. [PMID: 39211582 PMCID: PMC11350722 DOI: 10.1021/jacsau.4c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 09/04/2024]
Abstract
Protein synthesis and subsequent delivery to the target locations in cells are essential for their proper functions. Methods to label and distinguish newly synthesized proteins from existing ones are critical to assess their differential properties, but such methods are lacking. We describe the first chemical genetics-based approach for selective labeling of existing and newly synthesized proteins that we termed as CG-SLENP. Using HaloTag in-frame fusion with lamin A (LA), we demonstrate that the two pools of proteins can be selectively labeled using CG-SLENP in living cells. We further employ our recently developed selective small molecule ligand LBL1 for LA to probe the potential differences between newly synthesized and existing LA. Our results show that LBL1 can differentially modulate these two pools of LA. These results indicate that the assembly states of newly synthesized LA are distinct from existing LA in living cells. The CG-SLENP method is potentially generalizable to study any cellular proteins.
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Affiliation(s)
- Jian Wang
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Bo Chao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Jake Piesner
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Felice Kelly
- Advanced
Light Microscopy Shared Resource, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Stefanie Kaech Petrie
- Department
of Neurology, Knight Cancer Institute, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Xiangshu Xiao
- Department
of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Bingbing X. Li
- Department
of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, United States
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5
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Prajapati D, Clegg JK, Mukherjee PS. Formation of a low-symmetry Pd 8 molecular barrel employing a hetero donor tetradentate ligand, and its use in the binding and extraction of C 70. Chem Sci 2024; 15:12502-12510. [PMID: 39118615 PMCID: PMC11304780 DOI: 10.1039/d4sc01332h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/21/2024] [Indexed: 08/10/2024] Open
Abstract
The majority of reported metallo-supramolecules are highly symmetric homoleptic assemblies of M x L y type, with a few reports on assemblies that are obtained using multicomponent self-assembly or using ambidentate ligands. Herein, we report the use of an unsymmetrical tetratopic ligand (Lun) containing pyridyl and imidazole donor sites in combination with a cis-protected Pd(ii) acceptor for the formation of a low-symmetry M8Lun 4 molecular barrel (UNMB). Four potential orientational isomeric (HHHH, HHHT, HHTT, and HTHT) molecular barrels can be anticipated for the M8Lun 4 type metallo-assemblies. However, the formation of an orientational isomer (HHTT) of the barrel was suggested from single-crystal X-ray diffraction and 1H NMR analysis of UNMB. Two large open apertures at terminals and the hydrophobic confined space surrounded by four aromatic panels of Lun make UNMB a potential host for bigger guests. UNMB encapsulates fullerenes C70 and C60 favoured by non-covalent interactions between the fullerenes and aromatic panels of the ligand molecules. Experimental and theoretical studies revealed that UNMB has the ability to bind C70 more strongly than its lower analogue C60. The stronger affinity of UNMB towards C70 was exploited to separate C70 from an equimolar mixture of C70 and C60. Moreover, C70 can be extracted from the C70⊂UNMB complex by toluene, and therefore, UNMB can be reused as a recyclable separating agent for C70 extraction.
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Affiliation(s)
- Dharmraj Prajapati
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore-560012 India
| | - Jack K Clegg
- School of Chemistry and Molecular Biosciences, The University of Queensland St. Lucia Queensland 4072 Australia
| | - Partha Sarathi Mukherjee
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore-560012 India
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6
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Sendker FL, Schlotthauer T, Mais CN, Lo YK, Girbig M, Bohn S, Heimerl T, Schindler D, Weinstein A, Metzger BP, Thornton JW, Pillai A, Bange G, Schuller JM, Hochberg GK. Frequent transitions in self-assembly across the evolution of a central metabolic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602260. [PMID: 39005358 PMCID: PMC11245102 DOI: 10.1101/2024.07.05.602260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs. This has led to the proposition that self-assembly may instead vary neutrally within protein families. The extent of such variation has been difficult to ascertain because quaternary structure has until recently been difficult to measure on large scales. Here, we employ mass photometry, phylogenetics, and structural biology to interrogate the evolution of homo-oligomeric assembly across the entire phylogeny of prokaryotic citrate synthases - an enzyme with a highly conserved function. We discover a menagerie of different assembly types that come and go over the course of evolution, including cases of parallel evolution and reversions from complex to simple assemblies. Functional experiments in vitro and in vivo indicate that evolutionary transitions between different assemblies do not strongly influence enzyme catalysis. Our work suggests that enzymes can wander relatively freely through a large space of possible assemblies and demonstrates the power of characterizing structure-function relationships across entire phylogenies.
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Affiliation(s)
- Franziska L. Sendker
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Tabea Schlotthauer
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Mathias Girbig
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Stefan Bohn
- Institute of Structural Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1 Neuherberg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- MaxGENESYS Biofoundry, Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Arielle Weinstein
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Brain P. Metzger
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Joseph W. Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Arvind Pillai
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Gert Bange
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-University Marburg; Hans-Meerwein-Str. 4, 35043 Marburg, Germany
| | - Jan M. Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-University Marburg; Hans-Meerwein-Str. 4, 35043 Marburg, Germany
| | - Georg K.A. Hochberg
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-University Marburg; Hans-Meerwein-Str. 4, 35043 Marburg, Germany
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7
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List JM. Open Problems in Computational Historical Linguistics. OPEN RESEARCH EUROPE 2024; 3:201. [PMID: 38357681 PMCID: PMC10864822 DOI: 10.12688/openreseurope.16804.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/30/2024] [Indexed: 02/16/2024]
Abstract
Problems constitute the starting point of all scientific research. The essay reflects on the different kinds of problems that scientists address in their research and discusses a list of 10 problems for the field of computational historical linguistics, that was proposed throughout 2019 in a series of blog posts (see http://phylonetworks.blogspot.com/). In contrast to problems identified in different contexts, these problems were considered to be solvable, but no solution could be proposed back then. By discussing the problems in the light of developments that have been made in the field during the past five years, a modified list is proposed that takes new insights into account but also finds that the majority of the problems has not yet been solved.
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Affiliation(s)
- Johann-Mattis List
- Chair of Multilingual Computational Linguistics, University of Passau, Passau, Bavaria, 94032, Germany
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
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8
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Jhaveri A, Loggia S, Qian Y, Johnson ME. Discovering optimal kinetic pathways for self-assembly using automatic differentiation. Proc Natl Acad Sci U S A 2024; 121:e2403384121. [PMID: 38691585 PMCID: PMC11087789 DOI: 10.1073/pnas.2403384121] [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: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 05/03/2024] Open
Abstract
Macromolecular complexes are often composed of diverse subunits. The self-assembly of these subunits is inherently nonequilibrium and must avoid kinetic traps to achieve high yield over feasible timescales. We show how the kinetics of self-assembly benefits from diversity in subunits because it generates an expansive parameter space that naturally improves the "expressivity" of self-assembly, much like a deeper neural network. By using automatic differentiation algorithms commonly used in deep learning, we searched the parameter spaces of mass-action kinetic models to identify classes of kinetic protocols that mimic biological solutions for productive self-assembly. Our results reveal how high-yield complexes that easily become kinetically trapped in incomplete intermediates can instead be steered by internal design of rate-constants or external and active control of subunits to efficiently assemble. Internal design of a hierarchy of subunit binding rates generates self-assembly that can robustly avoid kinetic traps for all concentrations and energetics, but it places strict constraints on selection of relative rates. External control via subunit titration is more versatile, avoiding kinetic traps for any system without requiring molecular engineering of binding rates, albeit less efficiently and robustly. We derive theoretical expressions for the timescales of kinetic traps, and we demonstrate our optimization method applies not just for design but inference, extracting intersubunit binding rates from observations of yield-vs.-time for a heterotetramer. Overall, we identify optimal kinetic protocols for self-assembly as a powerful mechanism to achieve efficient and high-yield assembly in synthetic systems whether robustness or ease of "designability" is preferred.
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Affiliation(s)
- Adip Jhaveri
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Spencer Loggia
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Yian Qian
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Margaret E. Johnson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
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9
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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10
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Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell 2024; 187:999-1010.e15. [PMID: 38325366 DOI: 10.1016/j.cell.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
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Affiliation(s)
- Hugo Schweke
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Prasun Kumar
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Yoan Duhoo
- Protein Production and Structure Characterization Core Facility (PTPSP), School of Life Sciences, École polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin Dubreuil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, India.
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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11
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Fu C, Wang Z, Zhou X, Hu B, Li C, Yang P. Protein-based bioactive coatings: from nanoarchitectonics to applications. Chem Soc Rev 2024; 53:1514-1551. [PMID: 38167899 DOI: 10.1039/d3cs00786c] [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: 01/05/2024]
Abstract
Protein-based bioactive coatings have emerged as a versatile and promising strategy for enhancing the performance and biocompatibility of diverse biomedical materials and devices. Through surface modification, these coatings confer novel biofunctional attributes, rendering the material highly bioactive. Their widespread adoption across various domains in recent years underscores their importance. This review systematically elucidates the behavior of protein-based bioactive coatings in organisms and expounds on their underlying mechanisms. Furthermore, it highlights notable advancements in artificial synthesis methodologies and their functional applications in vitro. A focal point is the delineation of assembly strategies employed in crafting protein-based bioactive coatings, which provides a guide for their expansion and sustained implementation. Finally, the current trends, challenges, and future directions of protein-based bioactive coatings are discussed.
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Affiliation(s)
- Chengyu Fu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhengge Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Xingyu Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bowen Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chen Li
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Eastern HuaLan Avenue, Xinxiang, Henan 453003, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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12
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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13
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Bohl J, Moudjou M, Herzog L, Reine F, Sailer F, Klute H, Halgand F, Rest GVD, Boulard Y, Béringue V, Igel A, Rezaei H. The Smallest Infectious Substructure Encoding the Prion Strain Structural Determinant Revealed by Spontaneous Dissociation of Misfolded Prion Protein Assemblies. J Mol Biol 2023; 435:168280. [PMID: 37730082 DOI: 10.1016/j.jmb.2023.168280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
It is commonly accepted that the prion replicative propensity and strain structural determinant (SSD) are encoded in the fold of PrPSc amyloid fibril assemblies. By exploring the quaternary structure dynamicity of several prion strains, we revealed that all mammalian prion assemblies exhibit the generic property of spontaneously generating two sets of discreet infectious tetrameric and dimeric species differing significantly by their specific infectivity. By using perturbation approaches such as dilution and ionic strength variation, we demonstrated that these two oligomeric species were highly dynamic and evolved differently in the presence of chaotropic agents. In general, our observations of seven different prion strains from three distinct species highlight the high dynamicity of PrPSc assemblies as a common and intrinsic property of mammalian prions. The existence of such small infectious PrPSc species harboring the SSD indicates that the prion infectivity and the SSD are not restricted only to the amyloid fold but can also be encoded in other alternative quaternary structures. Such diversity in the quaternary structure of prion assemblies tends to indicate that the structure of PrPSc can be divided into two independent folding domains: a domain encoding the strain structural determinant and a second domain whose fold determines the type of quaternary structure that could adopt PrPSc assemblies.
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Affiliation(s)
- Jan Bohl
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France; ICP, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Mohammed Moudjou
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Laetitia Herzog
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Fabienne Reine
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Fiona Sailer
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Hannah Klute
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | | | | | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Vincent Béringue
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France.
| | - Angelique Igel
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France.
| | - Human Rezaei
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France.
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14
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Kilian M, Bischofs IB. Co-evolution at protein-protein interfaces guides inference of stoichiometry of oligomeric protein complexes by de novo structure prediction. Mol Microbiol 2023; 120:763-782. [PMID: 37777474 DOI: 10.1111/mmi.15169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
The quaternary structure with specific stoichiometry is pivotal to the specific function of protein complexes. However, determining the structure of many protein complexes experimentally remains a major bottleneck. Structural bioinformatics approaches, such as the deep learning algorithm Alphafold2-multimer (AF2-multimer), leverage the co-evolution of amino acids and sequence-structure relationships for accurate de novo structure and contact prediction. Pseudo-likelihood maximization direct coupling analysis (plmDCA) has been used to detect co-evolving residue pairs by statistical modeling. Here, we provide evidence that combining both methods can be used for de novo prediction of the quaternary structure and stoichiometry of a protein complex. We achieve this by augmenting the existing AF2-multimer confidence metrics with an interpretable score to identify the complex with an optimal fraction of native contacts of co-evolving residue pairs at intermolecular interfaces. We use this strategy to predict the quaternary structure and non-trivial stoichiometries of Bacillus subtilis spore germination protein complexes with unknown structures. Co-evolution at intermolecular interfaces may therefore synergize with AI-based de novo quaternary structure prediction of structurally uncharacterized bacterial protein complexes.
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Affiliation(s)
- Max Kilian
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- BioQuant Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Ilka B Bischofs
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- BioQuant Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
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15
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Zhang Z, Ye H, Cai F, Sun Y. Recent advances on the construction of long-wavelength emissive supramolecular coordination complexes for photo-diagnosis and therapy. Dalton Trans 2023; 52:15193-15202. [PMID: 37476886 DOI: 10.1039/d3dt01893h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Recently, metal-based drugs have attracted relentless interest in the biomedical field. However, their short excitation/emission wavelengths and unsatisfactory therapeutic efficiency limit their biological applications in vivo. Currently, the second near-infrared window (NIR-II, 1000-1700 nm) provides more accurate imaging and therapeutic options. Thus, there has been a constant focus on developing multifunctional NIR metal agents for imaging and therapy that have deeper tissue penetration. Fortunately, supramolecular coordination complexes (SCCs) formed by the coordination-driven self-assembly of NIR-II emissive ligands can address the above issues. Importantly, metal receptors with chemotherapeutic properties in SCCs can bind to luminescent ligands, thus becoming a versatile therapeutic platform for chemotherapy, imaging and phototherapy. In this context, we systematically summarize the evolution of NIR-II emissive SCCs for biomedical applications and discuss future challenges and prospects.
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Affiliation(s)
- Zhipeng Zhang
- Xianning Medical College, Hubei University of Science & Technology, Xianning 437000, P. R. China.
| | - Huan Ye
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, P. R. China
| | - Fei Cai
- Xianning Medical College, Hubei University of Science & Technology, Xianning 437000, P. R. China.
| | - Yao Sun
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
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16
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Li F, Grushin K, Coleman J, Pincet F, Rothman JE. Diacylglycerol-dependent hexamers of the SNARE-assembling chaperone Munc13-1 cooperatively bind vesicles. Proc Natl Acad Sci U S A 2023; 120:e2306086120. [PMID: 37883433 PMCID: PMC10623011 DOI: 10.1073/pnas.2306086120] [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: 04/14/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Munc13-1 is essential for vesicle docking and fusion at the active zone of synapses. Here, we report that Munc13-1 self-assembles into molecular clusters within diacylglycerol-rich microdomains present in phospholipid bilayers. Although the copy number of Munc13-1 molecules in these clusters has a broad distribution, a systematic Poisson analysis shows that this is most likely the result of two molecular species: monomers and mainly hexameric oligomers. Each oligomer is able to capture one vesicle independently. Hexamers have also been observed in crystals of Munc13-1 that form between opposed phospholipid bilayers [K. Grushin, R. V. Kalyana Sundaram, C. V. Sindelar, J. E. Rothman, Proc. Natl. Acad. Sci. U.S.A. 119, e2121259119 (2022)]. Mutations targeting the contacts stabilizing the crystallographic hexagons also disrupt the isolated hexamers, suggesting they are identical. Additionally, these mutations also convert vesicle binding from a cooperative to progressive mode. Our study provides an independent approach showing that Munc13-1 can form mainly hexamers on lipid bilayers each capable of vesicle capture.
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Affiliation(s)
- Feng Li
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT06520
- Nanobiology Institute, School of Medicine, Yale University, West Haven, CT06516
| | - Kirill Grushin
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT06520
- Nanobiology Institute, School of Medicine, Yale University, West Haven, CT06516
| | - Jeff Coleman
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT06520
- Nanobiology Institute, School of Medicine, Yale University, West Haven, CT06516
| | - Frederic Pincet
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT06520
- Nanobiology Institute, School of Medicine, Yale University, West Haven, CT06516
- Laboratoire de Physique de l’Ecole normale supérieure, Département de Physique, Ecole Normale Supérieure, Université Paris Sciences & Lettres CNRS, Sorbonne Université, Université de Paris, ParisF-75005, France
| | - James E. Rothman
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT06520
- Nanobiology Institute, School of Medicine, Yale University, West Haven, CT06516
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17
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Ciulla MG, Massironi A, Sugni M, Ensign MA, Marzorati S, Forouharshad M. Recent Advances in the Development of Biomimetic Materials. Gels 2023; 9:833. [PMID: 37888406 PMCID: PMC10606425 DOI: 10.3390/gels9100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
In this review, we focused on recent efforts in the design and development of materials with biomimetic properties. Innovative methods promise to emulate cell microenvironments and tissue functions, but many aspects regarding cellular communication, motility, and responsiveness remain to be explained. We photographed the state-of-the-art advancements in biomimetics, and discussed the complexity of a "bottom-up" artificial construction of living systems, with particular highlights on hydrogels, collagen-based composites, surface modifications, and three-dimensional (3D) bioprinting applications. Fast-paced 3D printing and artificial intelligence, nevertheless, collide with reality: How difficult can it be to build reproducible biomimetic materials at a real scale in line with the complexity of living systems? Nowadays, science is in urgent need of bioengineering technologies for the practical use of bioinspired and biomimetics for medicine and clinics.
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Affiliation(s)
- Maria G. Ciulla
- Department of Chemistry, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy
| | - Alessio Massironi
- Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Matthew A. Ensign
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Stefania Marzorati
- Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Mahdi Forouharshad
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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18
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Jhaveri A, Loggia S, Qian Y, Johnson ME. Discovering optimal kinetic pathways for self-assembly using automatic differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555551. [PMID: 37693527 PMCID: PMC10491160 DOI: 10.1101/2023.08.30.555551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
During self-assembly of macromolecules ranging from ribosomes to viral capsids, the formation of long-lived intermediates or kinetic traps can dramatically reduce yield of the functional products. Understanding biological mechanisms for avoiding traps and efficiently assembling is essential for designing synthetic assembly systems, but learning optimal solutions requires numerical searches in high-dimensional parameter spaces. Here, we exploit powerful automatic differentiation algorithms commonly employed by deep learning frameworks to optimize physical models of reversible self-assembly, discovering diverse solutions in the space of rate constants for 3-7 subunit complexes. We define two biologically-inspired protocols that prevent kinetic trapping through either internal design of subunit binding kinetics or external design of subunit titration in time. Our third protocol acts to recycle intermediates, mimicking energy-consuming enzymes. Preventative solutions via interface design are the most efficient and scale better with more subunits, but external control via titration or recycling are effective even for poorly evolved binding kinetics. Whilst all protocols can produce good solutions, diverse subunits always helps; these complexes access more efficient solutions when following external control protocols, and are simpler to design for internal control, as molecular interfaces do not need modification during assembly given sufficient variation in dimerization rates. Our results identify universal scaling in the cost of kinetic trapping, and provide multiple strategies for eliminating trapping and maximizing assembly yield across large parameter spaces.
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Affiliation(s)
| | | | - Yian Qian
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218
| | - Margaret E. Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218
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19
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Chen Q, Li Z, Lei Y, Chen Y, Tang H, Wu G, Sun B, Wei Y, Jiao T, Zhang S, Huang F, Wang L, Li H. The sharp structural switch of covalent cages mediated by subtle variation of directing groups. Nat Commun 2023; 14:4627. [PMID: 37532710 PMCID: PMC10397198 DOI: 10.1038/s41467-023-40255-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
It is considered a more formidable task to precisely control the self-assembled products containing purely covalent components, due to a lack of intrinsic templates such as transition metals to suppress entropy loss during self-assembly. Here, we attempt to tackle this challenge by using directing groups. That is, the self-assembly products of condensing a 1:2 mixture of a tetraformyl and a biamine can be precisely controlled by slightly changing the substituent groups in the aldehyde precursor. This is because different directing groups provide hydrogen bonds with different modes to the adjacent imine units, so that the building blocks are endowed with totally different conformations. Each conformation favors the formation of a specific product that is thus produced selectively, including chiral and achiral cages. These results of using a specific directing group to favor a target product pave the way for accomplishing atom economy in synthesizing purely covalent molecules without relying on toxic transition metal templates.
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Affiliation(s)
- Qiong Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Zhaoyong Li
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou, 310058, PR China
| | - Ye Lei
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Yixin Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Hua Tang
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Guangcheng Wu
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Bin Sun
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, PR China
| | - Yuxi Wei
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Tianyu Jiao
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China
| | - Songna Zhang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, PR China.
| | - Feihe Huang
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, PR China.
| | - Linjun Wang
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China.
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou, 310058, PR China.
| | - Hao Li
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, PR China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, PR China.
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20
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Lu J, Atochina-Vasserman EN, Maurya DS, Shalihin MI, Zhang D, Chenna SS, Adamson J, Liu M, Shah HUR, Shah H, Xiao Q, Queeley B, Ona NA, Reagan EK, Ni H, Sahoo D, Peterca M, Weissman D, Percec V. Screening Libraries to Discover Molecular Design Principles for the Targeted Delivery of mRNA with One-Component Ionizable Amphiphilic Janus Dendrimers Derived from Plant Phenolic Acids. Pharmaceutics 2023; 15:1572. [PMID: 37376020 DOI: 10.3390/pharmaceutics15061572] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/13/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Viral and synthetic vectors to deliver nucleic acids were key to the rapid development of extraordinarily efficient COVID-19 vaccines. The four-component lipid nanoparticles (LNPs), containing phospholipids, PEG-conjugated lipids, cholesterol, and ionizable lipids, co-assembled with mRNA via a microfluidic technology, are the leading nonviral delivery vector used by BioNTech/Pfizer and Moderna to access COVID-19 mRNA vaccines. LNPs exhibit a statistical distribution of their four components when delivering mRNA. Here, we report a methodology that involves screening libraries to discover the molecular design principles required to realize organ-targeted mRNA delivery and mediate activity with a one-component ionizable multifunctional amphiphilic Janus dendrimer (IAJD) derived from plant phenolic acids. IAJDs co-assemble with mRNA into monodisperse dendrimersome nanoparticles (DNPs) with predictable dimensions, via the simple injection of their ethanol solution in a buffer. The precise location of the functional groups in one-component IAJDs demonstrated that the targeted organs, including the liver, spleen, lymph nodes, and lung, are selected based on the hydrophilic region, while activity is associated with the hydrophobic domain of IAJDs. These principles, and a mechanistic hypothesis to explain activity, simplify the synthesis of IAJDs, the assembly of DNPs, handling, and storage of vaccines, and reduce price, despite employing renewable plant starting materials. Using simple molecular design principles will lead to increased accessibility to a large diversity of mRNA-based vaccines and nanotherapeutics.
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Affiliation(s)
- Juncheng Lu
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Elena N Atochina-Vasserman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Devendra S Maurya
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Muhammad Irhash Shalihin
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Dapeng Zhang
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Srijay S Chenna
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Jasper Adamson
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Matthew Liu
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Habib Ur Rehman Shah
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Honey Shah
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Qi Xiao
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Bryn Queeley
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Nathan A Ona
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Erin K Reagan
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Houping Ni
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Dipankar Sahoo
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Mihai Peterca
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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21
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Erba F, Di Paola L, Di Venere A, Mastrangelo E, Cossu F, Mei G, Minicozzi V. Head or tail? A molecular dynamics approach to the complex structure of TNF-associated factor TRAF2. Biomol Concepts 2023; 14:bmc-2022-0031. [PMID: 37377424 DOI: 10.1515/bmc-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Tumor necrosis factor receptor-associated factor proteins (TRAFs) are trimeric proteins that play a fundamental role in signaling, acting as intermediaries between the tumor necrosis factor (TNF) receptors and the proteins that transmit the downstream signal. The monomeric subunits of all the TRAF family members share a common tridimensional structure: a C-terminal globular domain and a long coiled-coil tail characterizing the N-terminal section. In this study, the dependence of the TRAF2 dynamics on the length of its tail was analyzed in silico. In particular, we used the available crystallographic structure of a C-terminal fragment of TRAF2 (168 out of 501 a.a.), TRAF2-C, and that of a longer construct, addressed as TRAF2-plus, that we have re-constructed using the AlphaFold2 code. The results indicate that the longer N-terminal tail of TRAF2-plus has a strong influence on the dynamics of the globular regions in the protein C-terminal head. In fact, the quaternary interactions among the TRAF2-C subunits change asymmetrically in time, while the movements of TRAF2-plus monomers are rather limited and more ordered than those of the shorter construct. Such findings shed a new light on the dynamics of TRAF subunits and on the protein mechanism in vivo, since TRAF monomer-trimer equilibrium is crucial for several reasons (receptor recognition, membrane binding, hetero-oligomerization).
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Affiliation(s)
- Fulvio Erba
- Department of Clinical Science and Translational Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Luisa Di Paola
- Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, University Campus Bio-Medico of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
| | - Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Eloise Mastrangelo
- National Research Council (IBF-CNR) Milan Unit, Institute of Biophysics, Via Celoria 26, 20133 Milan, Italy
| | - Federica Cossu
- National Research Council (IBF-CNR) Milan Unit, Institute of Biophysics, Via Celoria 26, 20133 Milan, Italy
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Velia Minicozzi
- Department of Physics and INFN, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy
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22
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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23
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Becchi M, Capelli R, Perego C, Pavan GM, Micheletti C. Density-tunable pathway complexity in a minimalistic self-assembly model. SOFT MATTER 2022; 18:8106-8116. [PMID: 36239129 DOI: 10.1039/d2sm00968d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
An open challenge in self-assembly is learning how to design systems that can be conditionally guided towards different target structures depending on externally-controlled conditions. Using a theoretical and numerical approach, here we discuss a minimalistic self-assembly model that can be steered towards different types of ordered constructs at the equilibrium by solely tuning a facile selection parameter, namely the density of building blocks. Metadynamics and Langevin dynamics simulations allow us to explore the behavior of the system in and out of equilibrium conditions. We show that the density-driven tunability is encoded in the pathway complexity of the system, and specifically in the competition between two different main self-assembly routes. A comprehensive set of simulations provides insight into key factors allowing to make one self-assembling pathway prevailing on the other (or vice versa), determining the selection of the final self-assembled products. We formulate and validate a practical criterion for checking whether a specific molecular design is predisposed for such density-driven tunability of the products, thus offering a new, broader perspective to realize and harness this facile extrinsic control of conditional self-assembly.
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Affiliation(s)
- Matteo Becchi
- Scuola Internazionale Superiore di Studi Avanzati - SISSA, via Bonomea 265, 34136 Trieste, Italy.
| | - Riccardo Capelli
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
- Department of Biosciences, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milano, Italy
| | - Claudio Perego
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati - SISSA, via Bonomea 265, 34136 Trieste, Italy.
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24
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Pillai AS, Hochberg GK, Thornton JW. Simple mechanisms for the evolution of protein complexity. Protein Sci 2022; 31:e4449. [PMID: 36107026 PMCID: PMC9601886 DOI: 10.1002/pro.4449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/26/2023]
Abstract
Proteins are tiny models of biological complexity: specific interactions among their many amino acids cause proteins to fold into elaborate structures, assemble with other proteins into higher-order complexes, and change their functions and structures upon binding other molecules. These complex features are classically thought to evolve via long and gradual trajectories driven by persistent natural selection. But a growing body of evidence from biochemistry, protein engineering, and molecular evolution shows that naturally occurring proteins often exist at or near the genetic edge of multimerization, allostery, and even new folds, so just one or a few mutations can trigger acquisition of these properties. These sudden transitions can occur because many of the physical properties that underlie these features are present in simpler proteins as fortuitous by-products of their architecture. Moreover, complex features of proteins can be encoded by huge arrays of sequences, so they are accessible from many different starting points via many possible paths. Because the bridges to these features are both short and numerous, random chance can join selection as a key factor in explaining the evolution of molecular complexity.
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Affiliation(s)
- Arvind S. Pillai
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Institute for Protein DesignUniversity of WashingtonSeattleWAUSA
| | - Georg K.A. Hochberg
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, Center for Synthetic MicrobiologyPhilipps University MarburgMarburgGermany
| | - Joseph W. Thornton
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Departments of Human Genetics and Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
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25
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Wicky BIM, Milles LF, Courbet A, Ragotte RJ, Dauparas J, Kinfu E, Tipps S, Kibler RD, Baek M, DiMaio F, Li X, Carter L, Kang A, Nguyen H, Bera AK, Baker D. Hallucinating symmetric protein assemblies. Science 2022; 378:56-61. [PMID: 36108048 PMCID: PMC9724707 DOI: 10.1126/science.add1964] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and C33 symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.
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Affiliation(s)
- B. I. M. Wicky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - L. F. Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - A. Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - R. J. Ragotte
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - J. Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - E. Kinfu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - S. Tipps
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - R. D. Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - M. Baek
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - F. DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - X. Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - L. Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - A. Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - H. Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - A. K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - D. Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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26
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Jacobs M, Bansal P, Shukla D, Schroeder CM. Understanding Supramolecular Assembly of Supercharged Proteins. ACS CENTRAL SCIENCE 2022; 8:1350-1361. [PMID: 36188338 PMCID: PMC9523778 DOI: 10.1021/acscentsci.2c00730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 06/16/2023]
Abstract
Ordered supramolecular assemblies have recently been created using electrostatic interactions between oppositely charged proteins. Despite recent progress, the fundamental mechanisms governing the assembly of oppositely supercharged proteins are not fully understood. Here, we use a combination of experiments and computational modeling to systematically study the supramolecular assembly process for a series of oppositely supercharged green fluorescent protein variants. We show that net charge is a sufficient molecular descriptor to predict the interaction fate of oppositely charged proteins under a given set of solution conditions (e.g., ionic strength), but the assembled supramolecular structures critically depend on surface charge distributions. Interestingly, our results show that a large excess of charge is necessary to nucleate assembly and that charged residues not directly involved in interprotein interactions contribute to a substantial fraction (∼30%) of the interaction energy between oppositely charged proteins via long-range electrostatic interactions. Dynamic subunit exchange experiments further show that relatively small, 16-subunit assemblies of oppositely charged proteins have kinetic lifetimes on the order of ∼10-40 min, which is governed by protein composition and solution conditions. Broadly, our results inform how protein supercharging can be used to create different ordered supramolecular assemblies from a single parent protein building block.
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Affiliation(s)
- Michael
I. Jacobs
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Prateek Bansal
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Materials Science and Engineering, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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27
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Slow Evolution toward “Super-Aggregation” of the Oligomers Formed through the Swapping of RNase A N-Termini: A Wish for Amyloidosis? Int J Mol Sci 2022; 23:ijms231911192. [PMID: 36232496 PMCID: PMC9569824 DOI: 10.3390/ijms231911192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Natively monomeric RNase A can oligomerize upon lyophilization from 40% acetic acid solutions or when it is heated at high concentrations in various solvents. In this way, it produces many dimeric or oligomeric conformers through the three-dimensional domain swapping (3D-DS) mechanism involving both RNase A N- or/and C-termini. Here, we found many of these oligomers evolving toward not negligible amounts of large derivatives after being stored for up to 15 months at 4 °C in phosphate buffer. We call these species super-aggregates (SAs). Notably, SAs do not originate from native RNase A monomer or from oligomers characterized by the exclusive presence of the C-terminus swapping of the enzyme subunits as well. Instead, the swapping of at least two subunits’ N-termini is mandatory to produce them. Through immunoblotting, SAs are confirmed to derive from RNase A even if they retain only low ribonucleolytic activity. Then, their interaction registered with Thioflavin-T (ThT), in addition to TEM analyses, indicate SAs are large and circular but not “amyloid-like” derivatives. This confirms that RNase A acts as an “auto-chaperone”, although it displays many amyloid-prone short segments, including the 16–22 loop included in its N-terminus. Therefore, we hypothesize the opening of RNase A N-terminus, and hence its oligomerization through 3D-DS, may represent a preliminary step favoring massive RNase A aggregation. Interestingly, this process is slow and requires low temperatures to limit the concomitant oligomers’ dissociation to the native monomer. These data and the hypothesis proposed are discussed in the light of protein aggregation in general, and of possible future applications to contrast amyloidosis.
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28
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Hundt N, Cole D, Hantke MF, Miller JJ, Struwe WB, Kukura P. Direct observation of the molecular mechanism underlying protein polymerization. SCIENCE ADVANCES 2022; 8:eabm7935. [PMID: 36044567 PMCID: PMC9432825 DOI: 10.1126/sciadv.abm7935] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Protein assembly is a main route to generating complexity in living systems. Revealing the relevant molecular details is challenging because of the intrinsic heterogeneity of species ranging from few to hundreds of molecules. Here, we use mass photometry to quantify and monitor the full range of actin oligomers during polymerization with single-molecule sensitivity. We find that traditional nucleation-based models cannot account for the observed distributions of actin oligomers. Instead, the key step of filament formation is a slow transition between distinct states of an actin filament mediated by cation exchange or ATP hydrolysis. The resulting model reproduces important aspects of actin polymerization, such as the critical concentration for filament formation and bulk growth behavior. Our results revise the mechanism of actin nucleation, shed light on the role and function of actin-associated proteins, and introduce a general and quantitative means to studying protein assembly at the molecular level.
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Affiliation(s)
- Nikolas Hundt
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Max F. Hantke
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Jack J. Miller
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PT, UK
- The PET Research Centre and The MR Research Centre, Aarhus University, Aarhus, Denmark
| | - Weston B. Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
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29
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Li S, Cai L, Hong M, Chen Q, Sun Q. Combinatorial Self‐Assembly of Coordination Cages with Systematically Fine‐Tuned Cavities for Efficient Co‐Encapsulation and Catalysis. Angew Chem Int Ed Engl 2022; 61:e202204732. [DOI: 10.1002/anie.202204732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 01/10/2023]
Affiliation(s)
- Shao‐Chuan Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 (P. R. China
- University of Chinese Academy of Sciences Beijing 100049 (P. R. China
| | - Li‐Xuan Cai
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 (P. R. China
- University of Chinese Academy of Sciences Beijing 100049 (P. R. China
| | - Maochun Hong
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 (P. R. China
- University of Chinese Academy of Sciences Beijing 100049 (P. R. China
| | - Qihui Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 (P. R. China
- University of Chinese Academy of Sciences Beijing 100049 (P. R. China
| | - Qing‐Fu Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 (P. R. China
- University of Chinese Academy of Sciences Beijing 100049 (P. R. China
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30
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Badonyi M, Marsh JA. Large protein complex interfaces have evolved to promote cotranslational assembly. eLife 2022; 11:79602. [PMID: 35899946 PMCID: PMC9365393 DOI: 10.7554/elife.79602] [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: 04/20/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this efficiency is by seeding assembly pathways during translation via the cotranslational assembly of subunits. While recent evidence suggests that such cotranslational assembly is widespread, little is known about the properties of protein complexes associated with the phenomenon. Here, using a combination of proteome-specific protein complex structures and publicly available ribosome profiling data, we show that cotranslational assembly is particularly common between subunits that form large intermolecular interfaces. To test whether large interfaces have evolved to promote cotranslational assembly, as opposed to cotranslational assembly being a non-adaptive consequence of large interfaces, we compared the sizes of first and last translated interfaces of heteromeric subunits in bacterial, yeast, and human complexes. When considering all together, we observe the N-terminal interface to be larger than the C-terminal interface 54% of the time, increasing to 64% when we exclude subunits with only small interfaces, which are unlikely to cotranslationally assemble. This strongly suggests that large interfaces have evolved as a means to maximise the chance of successful cotranslational subunit binding.
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Affiliation(s)
- Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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31
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Miller JE, Srinivasan Y, Dharmaraj NP, Liu A, Nguyen PL, Taylor SD, Yeates TO. Designing Protease-Triggered Protein Cages. J Am Chem Soc 2022; 144:12681-12689. [PMID: 35802879 DOI: 10.1021/jacs.2c02165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins that self-assemble into enclosed polyhedral cages, both naturally and by design, are garnering attention for their prospective utility in the fields of medicine and biotechnology. Notably, their potential for encapsulation and surface display are attractive for experiments that require protection and targeted delivery of cargo. The ability to control their opening or disassembly would greatly advance the development of protein nanocages into widespread molecular tools. Toward the development of protein cages that disassemble in a systematic manner and in response to biologically relevant stimuli, here we demonstrate a modular protein cage system that is opened by highly sequence-specific proteases, based on sequence insertions at strategically chosen loop positions in the protein cage subunits. We probed the generality of the approach in the context of protein cages built using the two prevailing methods of construction: genetic fusion between oligomeric components and (non-covalent) computational interface design between oligomeric components. Our results suggest that the former type of cage may be more amenable than the latter for endowing proteolytically controlled disassembly. We show that a successfully designed cage system, based on oligomeric fusion, is modular with regard to its triggering protease. One version of the cage is targeted by an asparagine protease implicated in cancer and Alzheimer's disease, whereas the second version is responsive to the blood-clotting protease, thrombin. The approach demonstrated here should guide future efforts to develop therapeutic vectors to treat disease states where protease induction or mis-regulation occurs.
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Affiliation(s)
- Justin E Miller
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Yashes Srinivasan
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Nithin P Dharmaraj
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Andrew Liu
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Phillip L Nguyen
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Scott D Taylor
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Todd O Yeates
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
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32
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Kleiner D, Shapiro Tuchman Z, Shmulevich F, Shahar A, Zarivach R, Kosloff M, Bershtein S. Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains. Protein Sci 2022; 31:e4352. [PMID: 35762725 PMCID: PMC9202080 DOI: 10.1002/pro.4352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/14/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022]
Abstract
Homomers are prevalent in bacterial proteomes, particularly among core metabolic enzymes. Homomerization is often key to function and regulation, and interfaces that facilitate the formation of homomeric enzymes are subject to intense evolutionary change. However, our understanding of the molecular mechanisms that drive evolutionary variation in homomeric complexes is still lacking. How is the diversification of protein interfaces linked to variation in functional regulation and structural integrity of homomeric complexes? To address this question, we studied quaternary structure evolution of bacterial methionine S-adenosyltransferases (MATs)-dihedral homotetramers formed along a large and conserved dimeric interface harboring two active sites, and a small, recently evolved, interdimeric interface. Here, we show that diversity in the physicochemical properties of small interfaces is directly linked to variability in the kinetic stability of MAT quaternary complexes and in modes of their functional regulation. Specifically, hydrophobic interactions within the small interface of Escherichia coli MAT render the functional homotetramer kinetically stable yet impose severe aggregation constraints on complex assembly. These constraints are alleviated by electrostatic interactions that accelerate dimer-dimer assembly. In contrast, Neisseria gonorrhoeae MAT adopts a nonfunctional dimeric state due to the low hydrophobicity of its small interface and the high flexibility of its active site loops, which perturbs small interface integrity. Remarkably, in the presence of methionine and ATP, N. gonorrhoeae MAT undergoes substrate-induced assembly into a functional tetrameric state. We suggest that evolution acts on the interdimeric interfaces of MATs to tailor the regulation of their activity and stability to unique organismal needs.
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Affiliation(s)
- Daniel Kleiner
- Department of Life SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Ziva Shapiro Tuchman
- The Department of Human Biology, Faculty of Natural SciencesUniversity of HaifaHaifaIsrael
| | - Fannia Shmulevich
- Department of Life SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Anat Shahar
- Ilse Katz Institute for Nanoscale Science & TechnologyBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Raz Zarivach
- Department of Life SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Macromolecular Crystallography and Cryo‐EM Research Center, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Mickey Kosloff
- The Department of Human Biology, Faculty of Natural SciencesUniversity of HaifaHaifaIsrael
| | - Shimon Bershtein
- Department of Life SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
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33
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Xuan JJ, Xia ZJ, Yan DN, Hu SJ, Zhou LP, Cai LX, Sun QF. Shape Complementary Coordination Self-Assembly of a Redox-Active Heteroleptic Complex. Inorg Chem 2022; 61:8854-8860. [PMID: 35642338 DOI: 10.1021/acs.inorgchem.2c00872] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here the coordination self-assembly of a new heteroleptic (bpyPd)4L1L22 coordination complex (1) from one novel pyridinium-functionalized bis-2,4,6-tris(pyridin-3-yl)-1,3,5-triazine (bis-3-TPT, L1) macrocyclic ligand, two separate 3-TPT (L2) ligands, and four cis-blocking bpyPd(NO3)2 (bpy = 2,2'-bipyridine). While homoleptic self-assemblies with either L1 or L2 gave dynamic mixtures of products, a single thermodynamic heteroleptic complex was obtained driven by the shape complementarity of building blocks. Moreover, the redox-active nature of the heteroleptic assembly facilitates the highly efficient catalytic aerobic photo-oxidation of aromatic secondary alcohols under mild conditions.
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Affiliation(s)
- Jin-Jin Xuan
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Zi-Jun Xia
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Dan-Ni Yan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Shao-Jun Hu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Li-Peng Zhou
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Li-Xuan Cai
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Qing-Fu Sun
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
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34
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Li SC, Cai LX, Hong M, Chen Q, Sun QF. Combinatorial Self‐Assembly of Coordination Cages with Systematically Fine‐Tuned Cavities for Efficient Co‐Encapsulation and Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shao-Chuan Li
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter State Key Laboratory of Strutral Chemistry CHINA
| | - Li-Xuan Cai
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter State Key Laboratory of Strutral Chemistry CHINA
| | - Maochun Hong
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter State Key Laboratory of Strutral Chemistry CHINA
| | - Qihui Chen
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter State Key Laboratory of Strutral Chemistry CHINA
| | - Qing-Fu Sun
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences State Key Laboratory of Structural Chemistry 155 Yangqiao Road West 350002 Fuzhou CHINA
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Abstract
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
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Affiliation(s)
- Kelly R Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Dalton T Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
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37
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Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution. Proc Natl Acad Sci U S A 2022; 119:e2113883119. [PMID: 35275794 PMCID: PMC8931234 DOI: 10.1073/pnas.2113883119] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
SignificanceWhy does evolution favor symmetric structures when they only represent a minute subset of all possible forms? Just as monkeys randomly typing into a computer language will preferentially produce outputs that can be generated by shorter algorithms, so the coding theorem from algorithmic information theory predicts that random mutations, when decoded by the process of development, preferentially produce phenotypes with shorter algorithmic descriptions. Since symmetric structures need less information to encode, they are much more likely to appear as potential variation. Combined with an arrival-of-the-frequent mechanism, this algorithmic bias predicts a much higher prevalence of low-complexity (high-symmetry) phenotypes than follows from natural selection alone and also explains patterns observed in protein complexes, RNA secondary structures, and a gene regulatory network.
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38
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Zhang D, Atochina-Vasserman EN, Lu J, Maurya DS, Xiao Q, Liu M, Adamson J, Ona N, Reagan EK, Ni H, Weissman D, Percec V. The Unexpected Importance of the Primary Structure of the Hydrophobic Part of One-Component Ionizable Amphiphilic Janus Dendrimers in Targeted mRNA Delivery Activity. J Am Chem Soc 2022; 144:4746-4753. [PMID: 35263098 DOI: 10.1021/jacs.2c00273] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viral and synthetic vectors for delivery of nucleic acids impacted genetic nanomedicine by aiding the rapid development of the extraordinarily efficient Covid-19 vaccines. Access to targeted delivery of nucleic acids is expected to expand the field of nanomedicine beyond most expectations. Both viral and synthetic vectors have advantages and disadvantages. The major advantage of the synthetic vectors is their unlimited synthetic capability. The four-component lipid nanoparticles (LNPs) are the leading nonviral vector for mRNA used by Pfizer and Moderna in Covid-19 vaccines. Their synthetic capacity inspired us to develop a one-component multifunctional sequence-defined ionizable amphiphilic Janus dendrimer (IAJD) delivery system for mRNA. The first experiments on IAJDs provided, through a rational-library design combined with orthogonal-modular accelerated synthesis and sequence control in their hydrophilic part, some of the most active synthetic vectors for the delivery of mRNA to lung. The second experiments employed a similar strategy, generating, by a less complex hydrophilic structure, a library of IAJDs targeting spleen, liver, and lung. Here, we report preliminary studies designing the hydrophobic region of IAJDs by using dissimilar alkyl lengths and demonstrate the unexpectedly important role of the primary structure of the hydrophobic part of IAJDs by increasing up to 90.2-fold the activity of targeted delivery of mRNA to spleen, lymph nodes, liver, and lung. The principles of the design strategy reported here and in previous publications indicate that IAJDs could have a profound impact on the future of genetic nanomedicine.
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Affiliation(s)
- Dapeng Zhang
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Elena N Atochina-Vasserman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Juncheng Lu
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Devendra S Maurya
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Qi Xiao
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Matthew Liu
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jasper Adamson
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Nathan Ona
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Erin K Reagan
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Houping Ni
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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39
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The properties of human disease mutations at protein interfaces. PLoS Comput Biol 2022; 18:e1009858. [PMID: 35120134 PMCID: PMC8849535 DOI: 10.1371/journal.pcbi.1009858] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/16/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022] Open
Abstract
The assembly of proteins into complexes and their interactions with other biomolecules are often vital for their biological function. While it is known that mutations at protein interfaces have a high potential to be damaging and cause human genetic disease, there has been relatively little consideration for how this varies between different types of interfaces. Here we investigate the properties of human pathogenic and putatively benign missense variants at homomeric (isologous and heterologous), heteromeric, DNA, RNA and other ligand interfaces, and at different regions in proteins with respect to those interfaces. We find that different types of interfaces vary greatly in their propensity to be associated with pathogenic mutations, with homomeric heterologous and DNA interfaces being particularly enriched in disease. We also find that residues that do not directly participate in an interface, but are close in three-dimensional space, show a significant disease enrichment. Finally, we observe that mutations at different types of interfaces tend to have distinct property changes when undergoing amino acid substitutions associated with disease, and that this is linked to substantial variability in their identification by computational variant effect predictors. Nearly all proteins interact with other molecules as part of their biological function. For example, proteins can interact with other copies of the same type of protein, with different proteins, with DNA, or with small ligand molecules. Many mutations at protein interfaces, the regions of proteins that interact with other molecules, are known to cause human genetic disease. In this study, we first investigate how different types of protein interfaces have different tendencies to be associated with disease. We also show that the closer a mutation is to an interface, the more likely it is to cause disease. Finally, we study how mutations at different types of interfaces tend to be associated with different changes in amino acid properties, which appears to influence our ability to computationally predict the effects of mutations. Ultimately, we hope that consideration of protein interface properties will eventually improve our ability to identify new disease-causing mutations.
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40
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Uncoupling Proteins and Regulated Proton Leak in Mitochondria. Int J Mol Sci 2022; 23:ijms23031528. [PMID: 35163451 PMCID: PMC8835771 DOI: 10.3390/ijms23031528] [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: 12/24/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
Abstract
Higher concentration of protons in the mitochondrial intermembrane space compared to the matrix results in an electrochemical potential causing the back flux of protons to the matrix. This proton transport can take place through ATP synthase complex (leading to formation of ATP) or can occur via proton transporters of the mitochondrial carrier superfamily and/or membrane lipids. Some mitochondrial proton transporters, such as uncoupling proteins (UCPs), transport protons as their general regulating function; while others are symporters or antiporters, which use the proton gradient as a driving force to co-transport other substrates across the mitochondrial inner membrane (such as phosphate carrier, a symporter; or aspartate/glutamate transporter, an antiporter). Passage (or leakage) of protons across the inner membrane to matrix from any route other than ATP synthase negatively impacts ATP synthesis. The focus of this review is on regulated proton transport by UCPs. Recent findings on the structure and function of UCPs, and the related research methodologies, are also critically reviewed. Due to structural similarity of members of the mitochondrial carrier superfamily, several of the known structural features are potentially expandable to all members. Overall, this report provides a brief, yet comprehensive, overview of the current knowledge in the field.
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41
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Schwarz PS, Tena-Solsona M, Dai K, Boekhoven J. Carbodiimide-fueled catalytic reaction cycles to regulate supramolecular processes. Chem Commun (Camb) 2022; 58:1284-1297. [PMID: 35014639 DOI: 10.1039/d1cc06428b] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Using molecular self-assembly, supramolecular chemists can create Gigadalton-structures with angstrom precision held together by non-covalent interactions. However, despite relying on the same molecular toolbox for self-assembly, these synthetic structures lack the complexity and sophistication of biological assemblies. Those assemblies are non-equilibrium structures that rely on the constant consumption of energy transduced from the hydrolysis of chemical fuels like ATP and GTP, which endows them with dynamic properties, e.g., temporal and spatial control and self-healing ability. Thus, to synthesize life-like materials, we have to find a reaction cycle that converts chemical energy to regulate self-assembly. We and others recently found that this can be done by a reaction cycle that hydrates carbodiimides. This feature article aims to provide an overview of how the energy transduced from carbodiimide hydration can alter the function of molecules and regulate molecular assemblies. The goal is to offer the reader design considerations for carbodiimide-driven reaction cycles to create a desired morphology or function of the assembly and ultimately to push chemically fueled self-assembly further towards the bottom-up synthesis of life.
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Affiliation(s)
- Patrick S Schwarz
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Marta Tena-Solsona
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Kun Dai
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany. .,Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748, Garching, Germany
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42
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Cieplak M, Mioduszewski Ł, Chwastyk M. Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins. Methods Mol Biol 2022; 2340:105-120. [PMID: 35167072 DOI: 10.1007/978-1-0716-1546-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We review the contact-based description of aggregation of intrinsically disordered proteins in coarse-grained and all-atom models. We consider polyglutamines and polyalanines at various concentrations of the peptides. We also study associations of two chains of α-synuclein and up to 20 chains of a 12-residue-long segment of protein tau. We demonstrate that the total number of two-chain association events (in an aggregate that comprises at least two chains) provides a useful measure of the propensity to aggregate. This measure is consistent, for instance, with the previously reported mass spectroscopy data. The distribution of the number of association events is given essentially by a power law as a function of the duration of these events. The corresponding exponent depends on the protein and the temperature but not on the concentration of the proteins.
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Affiliation(s)
- Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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43
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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44
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Schröder T, Bange S, Schedlbauer J, Steiner F, Lupton JM, Tinnefeld P, Vogelsang J. How Blinking Affects Photon Correlations in Multichromophoric Nanoparticles. ACS NANO 2021; 15:18037-18047. [PMID: 34735135 DOI: 10.1021/acsnano.1c06649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A single chromophore can only emit a maximum of one single photon per excitation cycle. This limitation results in a phenomenon commonly referred to as photon antibunching (pAB). When multiple chromophores contribute to the fluorescence measured, the degree of pAB has been used as a metric to "count" the number of chromophores. But the fact that chromophores can switch randomly between bright and dark states also impacts pAB and can lead to incorrect chromophore numbers being determined from pAB measurements. By both simulations and experiment, we demonstrate how pAB is affected by independent and collective chromophore blinking, enabling us to formulate universal guidelines for correct interpretation of pAB measurements. We use DNA-origami nanostructures to design multichromophoric model systems that exhibit either independent or collective chromophore blinking. Two approaches are presented that can distinguish experimentally between these two blinking mechanisms. The first one utilizes the different excitation intensity dependence on the blinking mechanisms. The second approach exploits the fact that collective blinking implies energy transfer to a quenching moiety, which is a time-dependent process. In pulsed-excitation experiments, the degree of collective blinking can therefore be altered by time gating the fluorescence photon stream, enabling us to extract the energy-transfer rate to a quencher. The ability to distinguish between different blinking mechanisms is valuable in materials science, such as for multichromophoric nanoparticles like conjugated-polymer chains as well as in biophysics, for example, for quantitative analysis of protein assemblies by counting chromophores.
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Affiliation(s)
- Tim Schröder
- Department Chemie and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Sebastian Bange
- Institut für Experimentelle und Angewandte Physik and Regensburg Center for Ultrafast Nanoscopy (RUN), Universität Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Jakob Schedlbauer
- Institut für Experimentelle und Angewandte Physik and Regensburg Center for Ultrafast Nanoscopy (RUN), Universität Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Florian Steiner
- Department Chemie and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - John M Lupton
- Institut für Experimentelle und Angewandte Physik and Regensburg Center for Ultrafast Nanoscopy (RUN), Universität Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Jan Vogelsang
- Institut für Experimentelle und Angewandte Physik and Regensburg Center for Ultrafast Nanoscopy (RUN), Universität Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
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45
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Hummert J, Yserentant K, Fink T, Euchner J, Ho YX, Tashev SA, Herten DP. Photobleaching step analysis for robust determination of protein complex stoichiometries. Mol Biol Cell 2021; 32:ar35. [PMID: 34586828 PMCID: PMC8693960 DOI: 10.1091/mbc.e20-09-0568] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
The counting of discrete photobleaching steps in fluorescence microscopy is ideally suited to study protein complex stoichiometry in situ. The counting range of photobleaching step analysis has been significantly improved with more-sophisticated algorithms for step detection, albeit at an increasing computational cost and with the necessity for high-quality data. Here, we address concerns regarding robustness, automation, and experimental validation, optimizing both data acquisition and analysis. To make full use of the potential of photobleaching step analysis, we evaluate various labeling strategies with respect to their molecular brightness, photostability, and photoblinking. The developed analysis algorithm focuses on automation and computational efficiency. Moreover, we validate the developed methods with experimental data acquired on DNA origami labeled with defined fluorophore numbers, demonstrating counting of up to 35 fluorophores. Finally, we show the power of the combination of optimized trace acquisition and automated data analysis by counting labeled nucleoporin 107 in nuclear pore complexes of intact U2OS cells. The successful in situ application promotes this framework as a new resource enabling cell biologists to robustly determine the stoichiometries of molecular assemblies at the single-molecule level in an automated manner.
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Affiliation(s)
- Johan Hummert
- Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, B152TT UK
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, Birmingham, B15 2TT UK
| | - Klaus Yserentant
- Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, D-69120 Heidelberg, Germany
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, B152TT UK
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, Birmingham, B15 2TT UK
| | - Theresa Fink
- Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
| | - Jonas Euchner
- Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, B152TT UK
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, Birmingham, B15 2TT UK
| | - Yin Xin Ho
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, B152TT UK
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, Birmingham, B15 2TT UK
| | - Stanimir Asenov Tashev
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, B152TT UK
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, Birmingham, B15 2TT UK
| | - Dirk-Peter Herten
- Institute of Physical Chemistry, Heidelberg University, D-69120 Heidelberg, Germany
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, B152TT UK
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, Birmingham, B15 2TT UK
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To P, Whitehead B, Tarbox HE, Fried SD. Nonrefoldability is Pervasive Across the E. coli Proteome. J Am Chem Soc 2021; 143:11435-11448. [PMID: 34308638 DOI: 10.1021/jacs.1c03270] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Decades of research on protein folding have primarily focused on a subset of small proteins that can reversibly refold from a denatured state. However, these studies have generally not been representative of the complexity of natural proteomes, which consist of many proteins with complex architectures and domain organizations. Here, we introduce an experimental approach to probe protein refolding kinetics for whole proteomes using mass spectrometry-based proteomics. Our study covers the majority of the soluble E. coli proteome expressed during log-phase growth, and among this group, we find that one-third of the E. coli proteome is not intrinsically refoldable on physiological time scales, a cohort that is enriched with certain fold-types, domain organizations, and other biophysical features. We also identify several properties and fold-types that are correlated with slow refolding on the minute time scale. Hence, these results illuminate when exogenous factors and processes, such as chaperones or cotranslational folding, might be required for efficient protein folding.
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Affiliation(s)
- Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Briana Whitehead
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Haley E Tarbox
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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48
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Feyh R, Waeber NB, Prinz S, Giammarinaro PI, Bange G, Hochberg G, Hartmann RK, Altegoer F. Structure and mechanistic features of the prokaryotic minimal RNase P. eLife 2021; 10:70160. [PMID: 34180399 PMCID: PMC8266387 DOI: 10.7554/elife.70160] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by ribonuclease P (RNase P) is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here, we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-electron microscopy, revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.
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Affiliation(s)
- Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nadine B Waeber
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Pietro Ivan Giammarinaro
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg Hochberg
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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49
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Dapkūnas J, Olechnovič K, Venclovas Č. Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction. Proteins 2021; 89:1834-1843. [PMID: 34176161 PMCID: PMC9292421 DOI: 10.1002/prot.26167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/08/2023]
Abstract
The goal of CASP experiments is to monitor the progress in the protein structure prediction field. During the 14th CASP edition we aimed to test our capabilities of predicting structures of protein complexes. Our protocol for modeling protein assemblies included both template‐based modeling and free docking. Structural templates were identified using sensitive sequence‐based searches. If sequence‐based searches failed, we performed structure‐based template searches using selected CASP server models. In the absence of reliable templates we applied free docking starting from monomers generated by CASP servers. We evaluated and ranked models of protein complexes using an improved version of our protein structure quality assessment method, VoroMQA, taking into account both interaction interface and global structure scores. If reliable templates could be identified, generally accurate models of protein assemblies were generated with the exception of an antibody‐antigen interaction. The success of free docking mainly depended on the accuracy of initial subunit models and on the scoring of docking solutions. To put our overall results in perspective, we analyzed our performance in the context of other CASP groups. Although the subunits in our assembly models often were not of the top quality, these models had, overall, the best‐predicted intersubunit interfaces according to several accuracy measures. We attribute our relative success primarily to the emphasis on the interaction interface when modeling and scoring.
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Affiliation(s)
- Justas Dapkūnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kliment Olechnovič
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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50
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Di Venere A, Nicolai E, Minicozzi V, Caccuri AM, Di Paola L, Mei G. The Odd Faces of Oligomers: The Case of TRAF2-C, A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor. Int J Mol Sci 2021; 22:ijms22115871. [PMID: 34070875 PMCID: PMC8198530 DOI: 10.3390/ijms22115871] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022] Open
Abstract
TNF Receptor Associated Factor 2 (TRAF2) is a trimeric protein that belongs to the TNF receptor associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding and for its interaction with other proteins involved in the TNFR signaling. The monomer-trimer equilibrium of a C- terminal domain truncated form of TRAF2 (TRAF2-C), plays also a relevant role in binding the membrane, causing inward vesiculation. In this study, we have investigated the conformational dynamics of TRAF2-C through circular dichroism, fluorescence, and dynamic light scattering, performing temperature-dependent measurements. The data indicate that the protein retains its oligomeric state and most of its secondary structure, while displaying a significative increase in the heterogeneity of the tyrosines signal, increasing the temperature from ≈15 to ≈35 °C. The peculiar crowding of tyrosine residues (12 out of 18) at the three subunit interfaces and the strong dependence on the trimer concentration indicate that such conformational changes mainly involve the contact areas between each pair of monomers, affecting the oligomeric state. Molecular dynamic simulations in this temperature range suggest that the interfaces heterogeneity is an intrinsic property of the trimer that arises from the continuous, asymmetric approaching and distancing of its subunits. Such dynamics affect the results of molecular docking on the external protein surface using receptor peptides, indicating that the TRAF2-receptor interaction in the solution might not involve three subunits at the same time, as suggested by the static analysis obtainable from the crystal structure. These findings shed new light on the role that the TRAF2 oligomeric state might have in regulating the protein binding activity in vivo.
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Affiliation(s)
- Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
| | - Eleonora Nicolai
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
| | - Velia Minicozzi
- Department of Physics, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Anna Maria Caccuri
- Department of Chemistry, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Luisa Di Paola
- Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, University Campus Bio-Medico of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
- Correspondence: (L.D.P.); (G.M.)
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
- Correspondence: (L.D.P.); (G.M.)
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