1
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Schnettler JD, Wang MS, Gantz M, Bunzel HA, Karas C, Hollfelder F, Hecht MH. Selection of a promiscuous minimalist cAMP phosphodiesterase from a library of de novo designed proteins. Nat Chem 2024; 16:1200-1208. [PMID: 38702405 PMCID: PMC11230910 DOI: 10.1038/s41557-024-01490-4] [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: 02/13/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
Abstract
The ability of unevolved amino acid sequences to become biological catalysts was key to the emergence of life on Earth. However, billions of years of evolution separate complex modern enzymes from their simpler early ancestors. To probe how unevolved sequences can develop new functions, we use ultrahigh-throughput droplet microfluidics to screen for phosphoesterase activity amidst a library of more than one million sequences based on a de novo designed 4-helix bundle. Characterization of hits revealed that acquisition of function involved a large jump in sequence space enriching for truncations that removed >40% of the protein chain. Biophysical characterization of a catalytically active truncated protein revealed that it dimerizes into an α-helical structure, with the gain of function accompanied by increased structural dynamics. The identified phosphodiesterase is a manganese-dependent metalloenzyme that hydrolyses a range of phosphodiesters. It is most active towards cyclic AMP, with a rate acceleration of ~109 and a catalytic proficiency of >1014 M-1, comparable to larger enzymes shaped by billions of years of evolution.
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Affiliation(s)
| | - Michael S Wang
- Department of Chemistry, Princeton University, Princeton, USA
| | - Maximilian Gantz
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - H Adrian Bunzel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christina Karas
- Department of Molecular Biology, Princeton University, Princeton, USA
| | | | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, USA.
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2
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Goldford JE, Smith HB, Longo LM, Wing BA, McGlynn SE. Primitive purine biosynthesis connects ancient geochemistry to modern metabolism. Nat Ecol Evol 2024; 8:999-1009. [PMID: 38519634 DOI: 10.1038/s41559-024-02361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/06/2024] [Indexed: 03/25/2024]
Abstract
An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.
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Affiliation(s)
- Joshua E Goldford
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Blue Marble Space Institute of Science, Seattle, WA, USA.
| | - Harrison B Smith
- Blue Marble Space Institute of Science, Seattle, WA, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Liam M Longo
- Blue Marble Space Institute of Science, Seattle, WA, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
| | - Shawn Erin McGlynn
- Blue Marble Space Institute of Science, Seattle, WA, USA.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Wako, Japan.
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3
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Zheng Z, Goncearenco A, Berezovsky IN. Back in time to the Gly-rich prototype of the phosphate binding elementary function. Curr Res Struct Biol 2024; 7:100142. [PMID: 38655428 PMCID: PMC11035071 DOI: 10.1016/j.crstbi.2024.100142] [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: 12/30/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.
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Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Igor N. Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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4
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Chisholm LO, Orlandi KN, Phillips SR, Shavlik MJ, Harms MJ. Ancestral Reconstruction and the Evolution of Protein Energy Landscapes. Annu Rev Biophys 2023; 53:10.1146/annurev-biophys-030722-125440. [PMID: 38134334 PMCID: PMC11192866 DOI: 10.1146/annurev-biophys-030722-125440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
A protein's sequence determines its conformational energy landscape. This, in turn, determines the protein's function. Understanding the evolution of new protein functions therefore requires understanding how mutations alter the protein energy landscape. Ancestral sequence reconstruction (ASR) has proven a valuable tool for tackling this problem. In ASR, one phylogenetically infers the sequences of ancient proteins, allowing characterization of their properties. When coupled to biophysical, biochemical, and functional characterization, ASR can reveal how historical mutations altered the energy landscape of ancient proteins, allowing the evolution of enzyme activity, altered conformations, binding specificity, oligomerization, and many other protein features. In this article, we review how ASR studies have been used to dissect the evolution of energy landscapes. We also discuss ASR studies that reveal how energy landscapes have shaped protein evolution. Finally, we propose that thinking about evolution from the perspective of an energy landscape can improve how we approach and interpret ASR studies. Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lauren O Chisholm
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Kona N Orlandi
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Biology, University of Oregon, Eugene, Oregon, USA
| | - Sophia R Phillips
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Michael J Shavlik
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Biology, University of Oregon, Eugene, Oregon, USA
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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5
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Tagami S. Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life. Biophys Physicobiol 2023; 20:e200026. [PMID: 38496239 PMCID: PMC10941967 DOI: 10.2142/biophysico.bppb-v20.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/29/2023] [Indexed: 03/19/2024] Open
Abstract
Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).
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Affiliation(s)
- Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
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6
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Anderson DM, Jayanthi LP, Gosavi S, Meiering EM. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. Front Mol Biosci 2023; 10:1021733. [PMID: 36845544 PMCID: PMC9945329 DOI: 10.3389/fmolb.2023.1021733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.
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Affiliation(s)
| | - Lakshmi P. Jayanthi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Elizabeth M. Meiering
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada,*Correspondence: Elizabeth M. Meiering,
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7
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Seal M, Weil-Ktorza O, Despotović D, Tawfik DS, Levy Y, Metanis N, Longo LM, Goldfarb D. Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains. J Am Chem Soc 2022; 144:14150-14160. [PMID: 35904499 PMCID: PMC9376946 DOI: 10.1021/jacs.2c03819] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance spectroscopy (EPR) to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif revealed the presence of dimers, even in the absence of RNA. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. DEER measurements of spin-diluted, doubly labeled peptides in solution indicated transient α-helical character. The distance distributions between spin labels in the dimer and the signatures of α-helical folding are consistent with the symmetric (HhH)2-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.
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Affiliation(s)
- Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orit Weil-Ktorza
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Dragana Despotović
- Department of Biomolecular Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dan S Tawfik
- Department of Biomolecular Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Casali Center for Applied Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Liam M Longo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, Washington 98104, United States
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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8
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Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022; 31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.
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Affiliation(s)
- Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Saacnicteh Toledo‐Patiño
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Lianet Noda‐García
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemRehovotIsrael
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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9
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Blaber M. Variable and Conserved Regions of Secondary Structure in the β-Trefoil Fold: Structure Versus Function. Front Mol Biosci 2022; 9:889943. [PMID: 35517858 PMCID: PMC9062101 DOI: 10.3389/fmolb.2022.889943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
β-trefoil proteins exhibit an approximate C3 rotational symmetry. An analysis of the secondary structure for members of this diverse superfamily of proteins indicates that it is comprised of remarkably conserved β-strands and highly-divergent turn regions. A fundamental “minimal” architecture can be identified that is devoid of heterogenous and extended turn regions, and is conserved among all family members. Conversely, the different functional families of β-trefoils can potentially be identified by their unique turn patterns (or turn “signature”). Such analyses provide clues as to the evolution of the β-trefoil family, suggesting a folding/stability role for the β-strands and a functional role for turn regions. This viewpoint can also guide de novo protein design of β-trefoil proteins having novel functionality.
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Affiliation(s)
- Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
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10
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Tenorio CA, Parker JB, Blaber M. Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways. Protein Sci 2022; 31:e4301. [PMID: 35481645 PMCID: PMC8996475 DOI: 10.1002/pro.4301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/02/2023]
Abstract
Successful de novo protein design ideally targets specific folding kinetics, stability thermodynamics, and biochemical functionality, and the simultaneous achievement of all these criteria in a single step design is challenging. Protein design is potentially simplified by separating the problem into two steps: (a) an initial design of a protein "scaffold" having appropriate folding kinetics and stability thermodynamics, followed by (b) appropriate functional mutation-possibly involving insertion of a peptide functional "cassette." This stepwise approach can also separate the orthogonal effects of the "stability/function" and "foldability/function" tradeoffs commonly observed in protein design. If the scaffold is a protein architecture having an exact rotational symmetry, then there is the potential for redundant folding nuclei and multiple equivalent sites of functionalization; thereby enabling broader functional adaptation. We describe such a "scaffold" and functional "cassette" design strategy applied to a β-trefoil threefold symmetric architecture and a heparin ligand functionality. The results support the availability of redundant folding nuclei within this symmetric architecture, and also identify a minimal peptide cassette conferring heparin affinity. The results also identify an energy barrier of destabilization that switches the protein folding pathway from monomeric to trimeric, thereby identifying another potential advantage of symmetric protein architecture in de novo design.
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Affiliation(s)
- Connie A. Tenorio
- Department of Biomedical Sciences Florida State University Tallahassee Florida USA
| | - Joseph B. Parker
- Department of Biomedical Sciences Florida State University Tallahassee Florida USA
| | - Michael Blaber
- Department of Biomedical Sciences Florida State University Tallahassee Florida USA
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11
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Tee WV, Wah Tan Z, Guarnera E, Berezovsky IN. Conservation and diversity in allosteric fingerprints of proteins for evolutionary-inspired engineering and design. J Mol Biol 2022; 434:167577. [PMID: 35395233 DOI: 10.1016/j.jmb.2022.167577] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for thorough investigation of its structural determinants and evolution. Learning directly from nature, we explored here allosteric communication in several major folds and repeat proteins, including α/β and β-barrels, β-propellers, Ig-like fold, ankyrin and α/β leucine-rich repeat proteins, which provide structural platforms for many different enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, modifications of the structure-driven signalling patterns via sequence-determined divergence to specific functions, as well as emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations will be instrumental in facilitating the engineering and de novo design of proteins with allosterically regulated functions, including development of therapeutic biologics. In particular, results described here may guide the identification of the optimal structural platforms (e.g. fold type, size, and oligomerization states) and the types of diversifications/perturbations, such as mutations, effector binding, and order-disorder transition. The tunable allosteric linkage across distant regions can be used as a pivotal component in the design/engineering of modular biological systems beyond the traditional scaffolding function.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.
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12
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Xu G, Kunzendorf A, Crotti M, Rozeboom HJ, Thunnissen AWH, Poelarends GJ. Gene Fusion and Directed Evolution to Break Structural Symmetry and Boost Catalysis by an Oligomeric C−C Bond‐Forming Enzyme. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guangcai Xu
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Andreas Kunzendorf
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Michele Crotti
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Henriëtte J. Rozeboom
- Molecular Enzymology Group Groningen Institute of Biomolecular Sciences and Biotechnology University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Andy‐Mark W. H. Thunnissen
- Molecular Enzymology Group Groningen Institute of Biomolecular Sciences and Biotechnology University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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13
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Longo LM, Kolodny R, McGlynn SE. Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich. PLoS Comput Biol 2022; 18:e1009833. [PMID: 35157697 PMCID: PMC8880906 DOI: 10.1371/journal.pcbi.1009833] [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: 01/07/2022] [Revised: 02/25/2022] [Accepted: 01/13/2022] [Indexed: 12/02/2022] Open
Abstract
As sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both 'β-trefoil bridging themes' (evolutionarily-related sequence segments) and 'β-trefoil-like motifs' (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself-namely, that it is a derived fold formed by 'budding' from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the evolution of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature's sewing table.
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Affiliation(s)
- Liam M. Longo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
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14
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Xu G, Kunzendorf A, Crotti M, Rozeboom HJ, Thunnissen AMWH, Poelarends GJ. Gene Fusion and Directed Evolution to Break Structural Symmetry and Boost Catalysis by an Oligomeric C-C Bond-Forming Enzyme. Angew Chem Int Ed Engl 2021; 61:e202113970. [PMID: 34890491 PMCID: PMC9306753 DOI: 10.1002/anie.202113970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 12/11/2022]
Abstract
Gene duplication and fusion are among the primary natural processes that generate new proteins from simpler ancestors. Here we adopted this strategy to evolve a promiscuous homohexameric 4-oxalocrotonate tautomerase (4-OT) into an efficient biocatalyst for enantioselective Michael reactions. We first designed a tandem-fused 4-OT to allow independent sequence diversification of adjacent subunits by directed evolution. This fused 4-OT was then subjected to eleven rounds of directed evolution to give variant 4-OT(F11), which showed an up to 320-fold enhanced activity for the Michael addition of nitromethane to cinnamaldehydes. Crystallographic analysis revealed that 4-OT(F11) has an unusual asymmetric trimeric architecture in which one of the monomers is flipped 180° relative to the others. This gene duplication and fusion strategy to break structural symmetry is likely to become an indispensable asset of the enzyme engineering toolbox, finding wide use in engineering oligomeric proteins.
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Affiliation(s)
- Guangcai Xu
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Andreas Kunzendorf
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Michele Crotti
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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15
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Parker JB, Tenorio CA, Blaber M. The ubiquitous buried water in the beta-trefoil architecture contributes to the folding nucleus and ~20% of the folding enthalpy. Protein Sci 2021; 30:2287-2297. [PMID: 34562298 DOI: 10.1002/pro.4192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/17/2023]
Abstract
The beta-trefoil protein architecture is characterized by three repeating "trefoil" motifs related by rotational symmetry and postulated to have evolved via gene duplication and fusion events. Despite this apparent structural symmetry, the primary and secondary structural elements typically exhibit pronounced asymmetric features. A survey of this family of proteins has revealed that among the most conserved symmetric structural elements is a ubiquitous buried solvent which participates in a bridging H-bond with three different beta-strands in each of the trefoil motifs. A computational analysis reported that these waters are likely associated with a substantial enthalpic contribution to overall stability. In this report, a Pro mutation is used to disrupt one of the water H-bond interactions to a main chain amide, and the effects upon stability and folding kinetics are determined. Combined with Ala mutations, the separate effects upon side chain truncation and H-bond deletion are analyzed in terms of stability and folding kinetics. The results show that these buried waters act to assemble a central folding nucleus, and are responsible for ~20% of the overall favorable enthalpy of folding.
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Affiliation(s)
- Joseph B Parker
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Connie A Tenorio
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
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16
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Youkharibache P. Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. Biomolecules 2021; 11:biom11091290. [PMID: 34572502 PMCID: PMC8470474 DOI: 10.3390/biom11091290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
The Ig fold has had a remarkable success in vertebrate evolution, with a presence in over 2% of human genes. The Ig fold is not just the elementary structural domain of antibodies and TCRs, it is also at the heart of a staggering 30% of immunologic cell surface receptors, making it a major orchestrator of cell–cell interactions. While BCRs, TCRs, and numerous Ig-based cell surface receptors form homo- or heterodimers on the same cell surface (in cis), many of them interface as ligand-receptors (checkpoints) on interacting cells (in trans) through their Ig domains. New Ig-Ig interfaces are still being discovered between Ig-based cell surface receptors, even in well-known families such as B7. What is largely ignored, however, is that the Ig fold itself is pseudosymmetric, a property that makes the Ig domain a versatile self-associative 3D structure and may, in part, explain its success in evolution, especially through its ability to bind in cis or in trans in the context of cell surface receptor–ligand interactions. In this paper, we review the Ig domains’ tertiary and quaternary pseudosymmetries, with particular attention to the newly identified double Ig fold in the solved CD19 molecular structure to highlight the underlying fundamental folding elements of Ig domains, i.e., Ig protodomains. This pseudosymmetric property of Ig domains gives us a decoding frame of reference to understand the fold, relate all Ig domain forms, single or double, and suggest new protein engineering avenues.
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17
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Abstract
Diverse bacterial lifestyle transitions are controlled by the nucleotide second messenger c-di-GMP, including virulence, motility, and biofilm formation. To control such fundamentally distinct processes, the set of genes under c-di-GMP control must have gone through several shifts during bacterial evolution. Here we show that the same σ–(c-di-GMP)–anti-σ switch has been co-opted during evolution to regulate distinct biological functions in unicellular and filamentous bacteria, controlling type IV pilus production in the genus Rubrobacter and the differentiation of reproductive hyphae into spores in Streptomyces. Moreover, we show that the anti-σ likely originated as a homodimer and evolved to become a monomer through an intragenic duplication event. This study thus describes the structural and functional evolution of a c-di-GMP regulatory switch. Filamentous actinobacteria of the genus Streptomyces have a complex lifecycle involving the differentiation of reproductive aerial hyphae into spores. We recently showed c-di-GMP controls this transition by arming a unique anti-σ, RsiG, to bind the sporulation-specific σ, WhiG. The Streptomyces venezuelae RsiG–(c-di-GMP)2–WhiG structure revealed that a monomeric RsiG binds c-di-GMP via two E(X)3S(X)2R(X)3Q(X)3D repeat motifs, one on each helix of an antiparallel coiled-coil. Here we show that RsiG homologs are found scattered throughout the Actinobacteria. Strikingly, RsiGs from unicellular bacteria descending from the most basal branch of the Actinobacteria are small proteins containing only one c-di-GMP binding motif, yet still bind their WhiG partners. Our structure of a Rubrobacter radiotolerans (RsiG)2–(c-di-GMP)2–WhiG complex revealed that these single-motif RsiGs are able to form an antiparallel coiled-coil through homodimerization, thereby allowing them to bind c-di-GMP similar to the monomeric twin-motif RsiGs. Further data show that in the unicellular actinobacterium R. radiotolerans, the (RsiG)2–(c-di-GMP)2–WhiG regulatory switch controls type IV pilus expression. Phylogenetic analysis indicates the single-motif RsiGs likely represent the ancestral state and an internal gene-duplication event gave rise to the twin-motif RsiGs inherited elsewhere in the Actinobacteria. Thus, these studies show how the anti-σ RsiG has evolved through an intragenic duplication event from a small protein carrying a single c-di-GMP binding motif, which functions as a homodimer, to a larger protein carrying two c-di-GMP binding motifs, which functions as a monomer. Consistent with this, our structures reveal potential selective advantages of the monomeric twin-motif anti-σ factors.
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18
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Heizinger L, Merkl R. Evidence for the preferential reuse of sub-domain motifs in primordial protein folds. Proteins 2021; 89:1167-1179. [PMID: 33957009 DOI: 10.1002/prot.26089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/15/2021] [Accepted: 04/28/2021] [Indexed: 11/06/2022]
Abstract
A comparison of protein backbones makes clear that not more than approximately 1400 different folds exist, each specifying the three-dimensional topology of a protein domain. Large proteins are composed of specific domain combinations and many domains can accommodate different functions. These findings confirm that the reuse of domains is key for the evolution of multi-domain proteins. If reuse was also the driving force for domain evolution, ancestral fragments of sub-domain size exist that are shared between domains possessing significantly different topologies. For the fully automated detection of putatively ancestral motifs, we developed the algorithm Fragstatt that compares proteins pairwise to identify fragments, that is, instantiations of the same motif. To reach maximal sensitivity, Fragstatt compares sequences by means of cascaded alignments of profile Hidden Markov Models. If the fragment sequences are sufficiently similar, the program determines and scores the structural concordance of the fragments. By analyzing a comprehensive set of proteins from the CATH database, Fragstatt identified 12 532 partially overlapping and structurally similar motifs that clustered to 134 unique motifs. The dissemination of these motifs is limited: We found only two domain topologies that contain two different motifs and generally, these motifs occur in not more than 18% of the CATH topologies. Interestingly, motifs are enriched in topologies that are considered ancestral. Thus, our findings suggest that the reuse of sub-domain sized fragments was relevant in early phases of protein evolution and became less important later on.
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Affiliation(s)
- Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
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19
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Blaber M. Cooperative hydrophobic core interactions in the β-trefoil architecture. Protein Sci 2021; 30:956-965. [PMID: 33686691 DOI: 10.1002/pro.4059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 11/09/2022]
Abstract
Symmetric protein architectures have a compelling aesthetic that suggests a plausible evolutionary process (i.e., gene duplication/fusion) yielding complex architecture from a simpler structural motif. Furthermore, symmetry inspires a practical approach to computational protein design that substantially reduces the combinatorial explosion problem, and may provide practical solutions for structure optimization. Despite such broad relevance, the role of structural symmetry in the key area of hydrophobic core-packing cooperativity has not been adequately studied. In the present report, the threefold rotational symmetry intrinsic to the β-trefoil architecture is shown to form a geometric basis for highly-cooperative core-packing interactions that both stabilize the local repeating motif and promote oligomerization/long-range contacts in the folding process. Symmetry in the β-trefoil structure also permits tolerance towards mutational drift that involves a structural quasi-equivalence at several key core positions.
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Affiliation(s)
- Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
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20
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Vrancken JPM, Noguchi H, Zhang KYJ, Tame JRH, Voet ARD. The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins 2021; 89:945-951. [PMID: 33713051 DOI: 10.1002/prot.26072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 01/17/2023]
Abstract
Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium-chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β-propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
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21
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Mylemans B, Voet AR, Tame JR. The Taming of the Screw: the natural and artificial development of β-propeller proteins. Curr Opin Struct Biol 2020; 68:48-54. [PMID: 33373773 DOI: 10.1016/j.sbi.2020.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/09/2020] [Accepted: 11/27/2020] [Indexed: 12/17/2022]
Abstract
Many proteins are found to possess repeated structural elements, which hint at ancient evolutionary origins and ongoing evolutionary processes. β-propeller proteins are a large family of such proteins, and a popular focus of structural analysis. This review highlights recent work to understand how they arose, and how they have developed into one of the most successful of all protein folds.
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Affiliation(s)
- Bram Mylemans
- Laboraotry for biomolecular modelling and design, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Arnout Rd Voet
- Protein Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan
| | - Jeremy Rh Tame
- Protein Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan.
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22
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Vrancken JPM, Tame JRH, Voet ARD. Development and applications of artificial symmetrical proteins. Comput Struct Biotechnol J 2020; 18:3959-3968. [PMID: 33335692 PMCID: PMC7734218 DOI: 10.1016/j.csbj.2020.10.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 12/28/2022] Open
Abstract
Since the determination of the first molecular models of proteins there has been interest in creating proteins artificially, but such methods have only become widely successful in the last decade. Gradual improvements over a long period of time have now yielded numerous examples of non-natural proteins, many of which are built from repeated elements. In this review we discuss the design of such symmetrical proteins and their various applications in chemistry and medicine.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
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23
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Mylemans B, Noguchi H, Deridder E, Lescrinier E, Tame JRH, Voet ARD. Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein. Protein Sci 2020; 29:2375-2386. [PMID: 33006397 DOI: 10.1002/pro.3961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 11/09/2022]
Abstract
The β-propeller fold is adopted by a sequentially diverse family of repeat proteins with apparent rotational symmetry. While the structure is mostly stabilized by hydrophobic interactions, an additional stabilization is provided by hydrogen bonds between the N-and C-termini, which are almost invariably part of the same β-sheet. This feature is often referred to as the "Velcro" closure. The positioning of the termini within a blade is variable and depends on the protein family. In order to investigate the influence of this location on protein structure, folding and stability, we created different circular permutants, and a circularized version, of the designer propeller protein named Pizza. This protein is perfectly symmetrical, possessing six identical repeats. While all mutants adopt the same structure, the proteins lacking the "Velcro" closure were found to be significantly less resistant to thermal and chemical denaturation. This could explain why such proteins are rarely observed in nature. Interestingly the most common "Velcro" configuration for this protein family was not the most stable among the Pizza variants tested. The circularized version shows dramatically improved stability, which could have implications for future applications.
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Affiliation(s)
| | | | - Els Deridder
- Department of Chemistry, KU Leuven, Leuven, Belgium
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24
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Blaber M. Conserved buried water molecules enable the β-trefoil architecture. Protein Sci 2020; 29:1794-1802. [PMID: 32542709 DOI: 10.1002/pro.3899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 12/24/2022]
Abstract
Available high-resolution crystal structures for the family of β-trefoil proteins in the structural databank were queried for buried waters. Such waters were classified as either: (a) unique to a particular domain, family, or superfamily or (b) conserved among all β-trefoil folds. Three buried waters conserved among all β-trefoil folds were identified. These waters are related by the threefold rotational pseudosymmetry characteristic of this protein architecture (representing three instances of an identical structural environment within each repeating trefoil-fold motif). The structural properties of this buried water are remarkable and include: residing in a cavity space no larger than a single water molecule, exhibiting a positional uncertainty (i.e., normalized B-factor) substantially lower than the average Cα atom, providing essentially ideal H-bonding geometry with three solvent-inaccessible main chain groups, simultaneously serving as a bridging H-bond for three different β-strands at a point of secondary structure divergence, and orienting conserved hydrophobic side chains to form a nascent core-packing group. Other published work supports an interpretation that these interactions are key to the formation of an efficient folding nucleus and folded thermostability. The fundamental threefold symmetric structural element of the β-trefoil fold is therefore, surprisingly, a buried water molecule.
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Affiliation(s)
- Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
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25
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Mylemans B, Laier I, Kamata K, Akashi S, Noguchi H, Tame JRH, Voet ARD. Structural plasticity of a designer protein sheds light on β-propeller protein evolution. FEBS J 2020; 288:530-545. [PMID: 32343866 DOI: 10.1111/febs.15347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/07/2020] [Accepted: 04/23/2020] [Indexed: 11/26/2022]
Abstract
β-propeller proteins are common in nature, where they are observed to adopt 4- to 10-fold internal rotational pseudo-symmetry. This size diversity can be explained by the evolutionary process of gene duplication and fusion. In this study, we investigated a distorted β-propeller protein, an apparent intermediate between two symmetries. From this template, we created a perfectly symmetric 9-bladed β-propeller named Cake, using computational design and ancestral sequence reconstruction. The designed repeat sequence was found to be capable of generating both 8-fold and 9-fold propellers which are highly stable. Cake variants with 2-10 identical copies of the repeat sequence were characterised by X-ray crystallography and in solution. They were found to be highly stable, and to self-assemble into 8- or 9-fold symmetrical propellers. These findings show that the β-propeller fold allows sufficient structural plasticity to permit a given blade to assemble different forms, a transition from even to odd changes in blade number, and provide a potential explanation for the wide diversity of repeat numbers observed in natural propeller proteins. DATABASE: Structural data are available in Protein Data Bank database under the accession numbers 6TJB, 6TJC, 6TJD, 6TJE, 6TJF, 6TJG, 6TJH and 6TJI.
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Affiliation(s)
| | - Ina Laier
- Department of Chemistry, KU Leuven, Belgium
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26
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Zhou W, Šmidlehner T, Jerala R. Synthetic biology principles for the design of protein with novel structures and functions. FEBS Lett 2020; 594:2199-2212. [PMID: 32324903 DOI: 10.1002/1873-3468.13796] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/29/2020] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Nature provides a large number of functional proteins that evolved during billions of years of evolution. The diversity of natural proteins encompasses versatile functions and more than a thousand different folds, which, however, represents only a tiny fraction of all possible folds and polypeptide sequences. Recent advances in the rational design of proteins demonstrate that it is possible to design de novo protein folds unseen in nature. Novel protein topologies have been designed based on similar principles as natural proteins using advanced computational modelling or modular construction principles, such as oligomerization domains. Designed proteins exhibit several interesting features such as extreme stability, designability of 3D topologies and folding pathways. Moreover, designed protein assemblies can implement symmetry similar to the viral capsids, while, on the other hand, single-chain pseudosymmetric designs can address each position independently. Recently, the design is expanding towards the introduction of new functions into designed proteins, and we may soon be able to design molecular machines.
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Affiliation(s)
- Weijun Zhou
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tamara Šmidlehner
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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27
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Tenorio CA, Parker JB, Blaber M. Oligomerization of a symmetric β-trefoil protein in response to folding nucleus perturbation. Protein Sci 2020; 29:1629-1640. [PMID: 32362013 DOI: 10.1002/pro.3877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 11/06/2022]
Abstract
Gene duplication and fusion events in protein evolution are postulated to be responsible for the common protein folds exhibiting internal rotational symmetry. Such evolutionary processes can also potentially yield regions of repetitive primary structure. Repetitive primary structure offers the potential for alternative definitions of critical regions, such as the folding nucleus (FN). In principle, more than one instance of the FN potentially enables an alternative folding pathway in the face of a subsequent deleterious mutation. We describe the targeted mutation of the carboxyl-terminal region of the (internally located) FN of the de novo designed purely-symmetric β-trefoil protein Symfoil-4P. This mutation involves wholesale replacement of a repeating trefoil-fold motif with a "blade" motif from a β-propeller protein, and postulated to trap that region of the Symfoil-4P FN in a nonproductive folding intermediate. The resulting protein (termed "Bladefoil") is shown to be cooperatively folding, but as a trimeric oligomer. The results illustrate how symmetric protein architectures have potentially diverse folding alternatives available to them, including oligomerization, when preferred pathways are perturbed.
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Affiliation(s)
- Connie A Tenorio
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Joseph B Parker
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
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28
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Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design. J Mol Biol 2020; 432:3898-3914. [PMID: 32330481 PMCID: PMC7322520 DOI: 10.1016/j.jmb.2020.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Natural evolution has generated an impressively diverse protein universe via duplication and recombination from a set of protein fragments that served as building blocks. The application of these concepts to the design of new proteins using subdomain-sized fragments from different folds has proven to be experimentally successful. To better understand how evolution has shaped our protein universe, we performed an all-against-all comparison of protein domains representing all naturally existing folds and identified conserved homologous protein fragments. Overall, we found more than 1000 protein fragments of various lengths among different folds through similarity network analysis. These fragments are present in very different protein environments and represent versatile building blocks for protein design. These data are available in our web server called F(old P)uzzle (fuzzle.uni-bayreuth.de), which allows to individually filter the dataset and create customized networks for folds of interest. We believe that our results serve as an invaluable resource for structural and evolutionary biologists and as raw material for the design of custom-made proteins.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Francisco Lobos
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dominik Lemm
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Saacnicteh Toledo-Patino
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Steffen Schmidt
- Max Planck Institute for Developmental Biology, Tübingen, Germany; Computational Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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29
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Tenorio CA, Longo LM, Parker JB, Lee J, Blaber M. Ab initio folding of a trefoil-fold motif reveals structural similarity with a β-propeller blade motif. Protein Sci 2020; 29:1172-1185. [PMID: 32142181 DOI: 10.1002/pro.3850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 01/05/2023]
Abstract
Many protein architectures exhibit evidence of internal rotational symmetry postulated to be the result of gene duplication/fusion events involving a primordial polypeptide motif. A common feature of such structures is a domain-swapped arrangement at the interface of the N- and C-termini motifs and postulated to provide cooperative interactions that promote folding and stability. De novo designed symmetric protein architectures have demonstrated an ability to accommodate circular permutation of the N- and C-termini in the overall architecture; however, the folding requirement of the primordial motif is poorly understood, and tolerance to circular permutation is essentially unknown. The β-trefoil protein fold is a threefold-symmetric architecture where the repeating ~42-mer "trefoil-fold" motif assembles via a domain-swapped arrangement. The trefoil-fold structure in isolation exposes considerable hydrophobic area that is otherwise buried in the intact β-trefoil trimeric assembly. The trefoil-fold sequence is not predicted to adopt the trefoil-fold architecture in ab initio folding studies; rather, the predicted fold is closely related to a compact "blade" motif from the β-propeller architecture. Expression of a trefoil-fold sequence and circular permutants shows that only the wild-type N-terminal motif definition yields an intact β-trefoil trimeric assembly, while permutants yield monomers. The results elucidate the folding requirements of the primordial trefoil-fold motif, and also suggest that this motif may sample a compact conformation that limits hydrophobic residue exposure, contains key trefoil-fold structural features, but is more structurally homologous to a β-propeller blade motif.
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Affiliation(s)
- Connie A Tenorio
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Liam M Longo
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Joseph B Parker
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jihun Lee
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
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30
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Khan F, Kurre D, Suguna K. Crystal structures of a β-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulfide bond-mediated dimeric forms. Glycobiology 2020; 30:474-488. [DOI: 10.1093/glycob/cwaa001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/12/2020] [Accepted: 01/17/2020] [Indexed: 01/02/2023] Open
Abstract
Abstractβ-Trefoil lectins are galactose/N-acetyl galactosamine specific lectins, which are widely distributed across all kingdoms of life and are known to perform several important functions. However, there is no report available on the characterization of these lectins from protozoans. We have performed structural and biophysical studies on a β-trefoil lectin from Entamoeba histolytica (EntTref), which exists as a mixture of monomers and dimers in solution. Further, we have determined the affinities of EntTref for rhamnose, galactose and different galactose-linked sugars. We obtained the crystal structure of EntTref in a sugar-free form (EntTref_apo) and a rhamnose-bound form (EntTref_rham). A novel Cys residue-mediated dimerization was revealed in the crystal structure of EntTref_apo while the structure of EntTref_rham provided the structural basis for the recognition of rhamnose by a β-trefoil lectin for the first time. To the best of our knowledge, this is the only report of the structural, functional and biophysical characterization of a β-trefoil lectin from a protozoan source and the first report of Cys-mediated dimerization in this class of lectins.
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Affiliation(s)
- Farha Khan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, CV Raman Rd, 560012, India
| | - Devanshu Kurre
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, CV Raman Rd, 560012, India
| | - K Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, CV Raman Rd, 560012, India
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31
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Berezovsky IN. Towards descriptor of elementary functions for protein design. Curr Opin Struct Biol 2019; 58:159-165. [PMID: 31352188 DOI: 10.1016/j.sbi.2019.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/18/2019] [Indexed: 11/18/2022]
Abstract
We review studies of the protein evolution that help to formulate rules for protein design. Acknowledging the fundamental importance of Dayhoff's provision on the emergence of functional proteins from short peptides, we discuss multiple evidences of the omnipresent partitioning of protein globules into structural/functional units, using which greatly facilitates the engineering and design efforts. Closed loops and elementary functional loops, which are descendants of ancient ring-like peptides that formed fist protein domains in agreement with Dayhoff's hypothesis, can be considered as basic units of protein structure and function. We argue that future developments in protein design approaches should consider descriptors of the elementary functions, which will help to complement designed scaffolds with functional signatures and flexibility necessary for their functions.
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Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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32
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Bliven SE, Lafita A, Rose PW, Capitani G, Prlić A, Bourne PE. Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Comput Biol 2019; 15:e1006842. [PMID: 31009453 PMCID: PMC6504099 DOI: 10.1371/journal.pcbi.1006842] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 05/07/2019] [Accepted: 01/29/2019] [Indexed: 01/04/2023] Open
Abstract
Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to the CE-Symm tool for systematically detecting and analyzing the internal symmetry and structural repeats in proteins. In addition to the accurate detection of internal symmetry, the tool is now capable of i) reporting the type of symmetry, ii) identifying the smallest repeating unit, iii) describing the arrangement of repeats with transformation operations and symmetry axes, and iv) comparing the similarity of all the internal repeats at the residue level. CE-Symm 2.0 helps the user investigate proteins with a robust and intuitive sequence-to-structure analysis, with many applications in protein classification, functional annotation and evolutionary studies. We describe the algorithmic extensions of the method and demonstrate its applications to the study of interesting cases of protein evolution. Many protein structures show a great deal of regularity. Even within single polypeptide chains, about 25% of proteins contain self-similar repeating structures, which can be organized in ring-like symmetric arrangements or linear open repeats. The repeats are often related, and thus comparing the sequence and structure of repeats can give an idea as to the early evolutionary history of a protein family. Additionally, the conservation and divergence of repeats can lead to insights about the function of the proteins. This work describes CE-Symm 2.0, a tool for the analysis of protein symmetry. The method automatically detects internal symmetry in protein structures and produces a multiple alignment of structural repeats. The algorithm is able to detect the geometric relationships between the repeats, including cyclic, dihedral, and polyhedral symmetries, translational repeats, and cases where multiple symmetry operators are applicable in a hierarchical manner. These complex relationships can then be visualized in a graphical interface as a complete structure, as a superposition of repeats, or as a multiple alignment of the protein sequence. CE-Symm 2.0 can be systematically used for the automatic detection of internal symmetry in protein structures, or as an interactive tool for the analysis of structural repeats.
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Affiliation(s)
- Spencer E. Bliven
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- Institute of Applied Simulation, Zurich University of Applied Science, Wädenswil, Switzerland
- * E-mail: (SEB), (AL)
| | - Aleix Lafita
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (SEB), (AL)
| | - Peter W. Rose
- RCSB Protein Data Bank, San Diego Supercomputing Center, University of California San Diego, La Jolla, California, United States of America
- Structural Bioinformatics Laboratory, San Diego Supercomputing Center, University of California San Diego, La Jolla, California, United States of America
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andreas Prlić
- RCSB Protein Data Bank, San Diego Supercomputing Center, University of California San Diego, La Jolla, California, United States of America
| | - Philip E. Bourne
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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33
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Wright JN, Wong WL, Harvey JA, Garnett JA, Itzhaki LS, Main ERG. Scalable Geometrically Designed Protein Cages Assembled via Genetically Encoded Split Inteins. Structure 2019; 27:776-784.e4. [PMID: 30879889 DOI: 10.1016/j.str.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 01/20/2023]
Abstract
Engineering proteins to assemble into user-defined structures is key in their development for biotechnological applications. However, designing generic rather than bespoke solutions is challenging. Here we describe an expandable recombinant assembly system that produces scalable protein cages via split intein-mediated native chemical ligation. Three types of component are used: two complementary oligomeric "half-cage" protein fusions and an extendable monomeric "linker" fusion. All are composed of modular protein domains chosen to fulfill the required geometries, with two orthogonal pairs of split intein halves to drive assembly when mixed. This combination enables both one-pot construction of two-component cages and stepwise assembly of larger three-component scalable cages. To illustrate the system's versatility, trimeric half-cages and linker constructs comprising consensus-designed repeat proteins were ligated in one-pot and stepwise reactions. Under mild conditions, rapid high-yielding ligations were obtained, from which discrete proteins cages were easily purified and shown to form the desired trigonal bipyramidal structures.
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Affiliation(s)
- James N Wright
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Wan Ling Wong
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Joseph A Harvey
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - James A Garnett
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ewan R G Main
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK.
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34
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Noguchi H, Addy C, Simoncini D, Wouters S, Mylemans B, Van Meervelt L, Schiex T, Zhang KYJ, Tame JRH, Voet ARD. Computational design of symmetrical eight-bladed β-propeller proteins. IUCRJ 2019; 6:46-55. [PMID: 30713702 PMCID: PMC6327176 DOI: 10.1107/s205225251801480x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/19/2018] [Indexed: 05/04/2023]
Abstract
β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.
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Affiliation(s)
- Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Christine Addy
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - David Simoncini
- MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France
| | - Staf Wouters
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Luc Van Meervelt
- Laboratory of Biomolecular Architecture, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Thomas Schiex
- MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Jeremy R. H. Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Arnout R. D. Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
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35
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ElGamacy M, Coles M, Lupas A. Asymmetric protein design from conserved supersecondary structures. J Struct Biol 2018; 204:380-387. [DOI: 10.1016/j.jsb.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
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36
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Investigation of protein quaternary structure via stoichiometry and symmetry information. PLoS One 2018; 13:e0197176. [PMID: 29864163 PMCID: PMC5986128 DOI: 10.1371/journal.pone.0197176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/27/2018] [Indexed: 11/30/2022] Open
Abstract
The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org/).
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37
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Noguchi H, Mylemans B, De Zitter E, Van Meervelt L, Tame JRH, Voet A. Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies. Biochem Biophys Res Commun 2018; 497:1038-1042. [PMID: 29481797 DOI: 10.1016/j.bbrc.2018.02.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 01/29/2023]
Abstract
β-propeller proteins are highly symmetrical, being composed of a repeated motif with four anti-parallel β-sheets arranged around a central axis. Recently we designed the first completely symmetrical β-propeller protein, Pizza6, consisting of six identical tandem repeats. Pizza6 is expected to prove a useful building block for bionanotechnology, and also a tool to investigate the folding and evolution of β-propeller proteins. Folding studies are made difficult by the high stability and the lack of buried Trp residues to act as monitor fluorophores, so we have designed and characterized several Trp-containing Pizza6 derivatives. In total four proteins were designed, of which three could be purified and characterized. Crystal structures confirm these mutant proteins maintain the expected structure, and a clear redshift of Trp fluorescence emission could be observed upon denaturation. Among the derivative proteins, Pizza6-AYW appears to be the most suitable model protein for future folding/unfolding kinetics studies as it has a comparable stability as natural β-propeller proteins.
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Affiliation(s)
- Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Elke De Zitter
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Luc Van Meervelt
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium.
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38
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Alva V, Lupas AN. From ancestral peptides to designed proteins. Curr Opin Struct Biol 2017; 48:103-109. [PMID: 29195087 DOI: 10.1016/j.sbi.2017.11.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 11/20/2017] [Indexed: 11/16/2022]
Abstract
The diversity of modern proteins arose through the combinatorial shuffling and differentiation of a limited number of autonomously folding domain prototypes, but the origin of these prototypes themselves has long remained poorly understood. In recent years, the proposal that they originated by repetition, accretion, and recombination from an ancestral set of peptides, which evolved as cofactors of RNA-based replication and catalysis, has gained wide acceptance, supported by the systematic identification of such ancestral peptides and the experimental recapitulation of the mechanisms by which they could have yielded the first folded proteins. Inspired by this evolutionary process, protein engineers have seized on design from pre-optimized peptide components as a powerful approach to generating proteins with novel topology and functionality.
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Affiliation(s)
- Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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39
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Designing repeat proteins: a modular approach to protein design. Curr Opin Struct Biol 2017; 45:116-123. [DOI: 10.1016/j.sbi.2017.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 01/01/2023]
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40
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Terada D, Voet ARD, Noguchi H, Kamata K, Ohki M, Addy C, Fujii Y, Yamamoto D, Ozeki Y, Tame JRH, Zhang KYJ. Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity. Sci Rep 2017; 7:5943. [PMID: 28724971 PMCID: PMC5517649 DOI: 10.1038/s41598-017-06332-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/12/2017] [Indexed: 01/24/2023] Open
Abstract
Computational protein design has advanced very rapidly over the last decade, but there remain few examples of artificial proteins with direct medical applications. This study describes a new artificial β-trefoil lectin that recognises Burkitt’s lymphoma cells, and which was designed with the intention of finding a basis for novel cancer treatments or diagnostics. The new protein, called “Mitsuba”, is based on the structure of the natural shellfish lectin MytiLec-1, a member of a small lectin family that uses unique sequence motifs to bind α-D-galactose. The three subdomains of MytiLec-1 each carry one galactose binding site, and the 149-residue protein forms a tight dimer in solution. Mitsuba (meaning “three-leaf” in Japanese) was created by symmetry constraining the structure of a MytiLec-1 subunit, resulting in a 150-residue sequence that contains three identical tandem repeats. Mitsuba-1 was expressed and crystallised to confirm the X-ray structure matches the predicted model. Mitsuba-1 recognises cancer cells that express globotriose (Galα(1,4)Galβ(1,4)Glc) on the surface, but the cytotoxicity is abolished.
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Affiliation(s)
- Daiki Terada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan.,Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Kenichi Kamata
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Mio Ohki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Christine Addy
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Fujii
- Department of Pharmacy, Graduate School of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298, Japan
| | - Daiki Yamamoto
- Laboratory of Glycobiology and Marine Biochemistry, Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa, 236-0027, Japan
| | - Yasuhiro Ozeki
- Laboratory of Glycobiology and Marine Biochemistry, Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa, 236-0027, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan.
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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41
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Structure-diverse Phylomer libraries as a rich source of bioactive hits from phenotypic and target directed screens against intracellular proteins. Curr Opin Chem Biol 2017; 38:127-133. [DOI: 10.1016/j.cbpa.2017.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 01/15/2023]
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42
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Lupas AN, Alva V. Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins. J Struct Biol 2017; 198:74-81. [DOI: 10.1016/j.jsb.2017.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 11/16/2022]
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43
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Structure prediction and functional analysis of a non-permutated lectin from Dioclea grandiflora. Biochimie 2016; 131:54-67. [DOI: 10.1016/j.biochi.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/19/2016] [Indexed: 01/22/2023]
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44
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Romero Romero ML, Rabin A, Tawfik DS. Funktionelle Proteine aus kurzen Peptiden: 50 Jahre nach Margaret Dayhoffs Hypothese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- M. Luisa Romero Romero
- Department of Biomolecular Sciences; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Avigayel Rabin
- Derzeitige Adresse: Department of Biological Chemistry, Alexander Silberman Inst. of Life Sciences; The Hebrew University of Jerusalem; Edmond J. Safra Campus Jerusalem 91904 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences; The Weizmann Institute of Science; Rehovot 76100 Israel
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45
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Romero Romero ML, Rabin A, Tawfik DS. Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50. Angew Chem Int Ed Engl 2016; 55:15966-15971. [PMID: 27865046 DOI: 10.1002/anie.201609977] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 01/08/2023]
Abstract
First and foremost: Margaret Dayhoff's 1966 hypothesis on the origin of proteins is now an accepted model for the emergence of large, globular, functional proteins from short, simple peptides. However, the fundamental question of how the first protein(s) emerged still stands. The tools and hypotheses pioneered by Dayhoff, and the over 65 million protein sequences and 12 000 structures known today, enable those who follow in her footsteps to address this question.
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Affiliation(s)
- M Luisa Romero Romero
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Avigayel Rabin
- Current address: Department of Biological Chemistry the Alexander Silberman Inst. of Life Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 91904, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
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46
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Zhu H, Sepulveda E, Hartmann MD, Kogenaru M, Ursinus A, Sulz E, Albrecht R, Coles M, Martin J, Lupas AN. Origin of a folded repeat protein from an intrinsically disordered ancestor. eLife 2016; 5:e16761. [PMID: 27623012 PMCID: PMC5074805 DOI: 10.7554/elife.16761] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
Repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. Many of these originated in a non-repetitive context as cofactors of RNA-based replication and catalysis, and required the RNA to assume their active conformation. In search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (TPR), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the putatively ancient ribosomal protein S20 (RPS20), which only becomes structured in the context of the ribosome. We evaluated the ability of the RPS20 hairpin to form a TPR fold by amplification and obtained structures identical to natural TPRs for variants with 2-5 point mutations per repeat. The mutations were neutral in the parent organism, suggesting that they could have been sampled in the course of evolution. TPRs could thus have plausibly arisen by amplification from an ancestral helical hairpin.
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Affiliation(s)
- Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Edgardo Sepulveda
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Manjunatha Kogenaru
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Astrid Ursinus
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eva Sulz
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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47
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Benedek A, Horváth A, Hirmondó R, Ozohanics O, Békési A, Módos K, Révész Á, Vékey K, Nagy GN, Vértessy BG. Potential steps in the evolution of a fused trimeric all-β dUTPase involve a catalytically competent fused dimeric intermediate. FEBS J 2016; 283:3268-86. [PMID: 27380921 DOI: 10.1111/febs.13800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 06/08/2016] [Accepted: 07/04/2016] [Indexed: 12/15/2022]
Abstract
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is essential for genome integrity. Interestingly, this enzyme from Drosophila virilis has an unusual form, as three monomer repeats are merged with short linker sequences, yielding a fused trimer-like dUTPase fold. Unlike homotrimeric dUTPases that are encoded by a single repeat dut gene copy, the three repeats of the D. virilis dut gene are not identical due to several point mutations. We investigated the potential evolutionary pathway that led to the emergence of this extant fused trimeric dUTPase in D. virilis. The herein proposed scenario involves two sequential gene duplications followed by sequence divergence amongst the dut repeats. This pathway thus requires the existence of a transient two-repeat-containing fused dimeric dUTPase intermediate. We identified the corresponding ancestral dUTPase single repeat enzyme together with its tandem repeat evolutionary intermediate and characterized their enzymatic function and structural stability. We additionally engineered and characterized artificial single or tandem repeat constructs from the extant enzyme form to investigate the influence of the emergent residue alterations on the formation of a functional assembly. The observed severely impaired stability and catalytic activity of these latter constructs provide a plausible explanation for evolutionary persistence of the extant fused trimeric D. virilis dUTPase form. For the ancestral homotrimeric and the fused dimeric intermediate forms, we observed strong catalytic and structural competence, verifying viability of the proposed evolutionary pathway. We conclude that the progression along the herein described evolutionary trajectory is determined by the retained potential of the enzyme for its conserved three-fold structural symmetry.
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Affiliation(s)
- András Benedek
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
| | - András Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Rita Hirmondó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Angéla Békési
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Módos
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ágnes Révész
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Vékey
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
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48
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Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types. Sci Rep 2016; 6:28344. [PMID: 27321048 PMCID: PMC4913266 DOI: 10.1038/srep28344] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/31/2016] [Indexed: 01/07/2023] Open
Abstract
MytiLec is a lectin, isolated from bivalves, with cytotoxic activity against cancer cell lines that express globotriaosyl ceramide, Galα(1,4)Galβ(1,4)Glcα1-Cer, on the cell surface. Functional analysis shows that the protein binds to the disaccharide melibiose, Galα(1,6)Glc, and the trisaccharide globotriose, Galα(1,4)Galβ(1,4)Glc. Recombinant MytiLec expressed in bacteria showed the same haemagglutinating and cytotoxic activity against Burkitt's lymphoma (Raji) cells as the native form. The crystal structure has been determined to atomic resolution, in the presence and absence of ligands, showing the protein to be a member of the β-trefoil family, but with a mode of ligand binding unique to a small group of related trefoil lectins. Each of the three pseudo-equivalent binding sites within the monomer shows ligand binding, and the protein forms a tight dimer in solution. An engineered monomer mutant lost all cytotoxic activity against Raji cells, but retained some haemagglutination activity, showing that the quaternary structure of the protein is important for its cellular effects.
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49
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Clark PL. How to Build a Complex, Functional Propeller Protein, From Parts. Trends Biochem Sci 2016; 41:290-292. [PMID: 26971075 DOI: 10.1016/j.tibs.2016.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 01/09/2023]
Abstract
By combining ancestral sequence reconstruction and in vitro evolution, Smock et al. identified single motifs that assemble into a functional five-bladed β-propeller, and a likely route for conversion into the more complex, extant single chain fusion. Interestingly, although sequence diversification destabilized five-motif fusions, it also destabilized aggregation-prone intermediates, increasing the level of functional protein in vivo.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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50
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Khersonsky O, Fleishman SJ. Why reinvent the wheel? Building new proteins based on ready-made parts. Protein Sci 2016; 25:1179-87. [PMID: 26821641 DOI: 10.1002/pro.2892] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/20/2016] [Accepted: 01/27/2016] [Indexed: 12/12/2022]
Abstract
We protein engineers are ambivalent about evolution: on the one hand, evolution inspires us with myriad examples of biomolecular binders, sensors, and catalysts; on the other hand, these examples are seldom well-adapted to the engineering tasks we have in mind. Protein engineers have therefore modified natural proteins by point substitutions and fragment exchanges in an effort to generate new functions. A counterpoint to such design efforts, which is being pursued now with greater success, is to completely eschew the starting materials provided by nature and to design new protein functions from scratch by using de novo molecular modeling and design. While important progress has been made in both directions, some areas of protein design are still beyond reach. To this end, we advocate a synthesis of these two strategies: by using design calculations to both recombine and optimize fragments from natural proteins, we can build stable and as of yet un-sampled structures, thereby granting access to an expanded repertoire of conformations and desired functions. We propose that future methods that combine phylogenetic analysis, structure and sequence bioinformatics, and atomistic modeling may well succeed where any one of these approaches has failed on its own.
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Affiliation(s)
- Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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