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Laurino P, Tóth-Petróczy Á, Meana-Pañeda R, Lin W, Truhlar DG, Tawfik DS. An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PLoS Biol 2016; 14:e1002396. [PMID: 26938925 PMCID: PMC4777477 DOI: 10.1371/journal.pbio.1002396] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/29/2016] [Indexed: 01/30/2023] Open
Abstract
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not only rare but also have a different topology and geometry. We further show that the canonical geometry is not dictated by a physical constraint--geometries found in noncanonical interactions have similar calculated bond energies. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes, with different cofactors and catalytic chemistries, from a common pre-LUCA (last universal common ancestor) ancestor that possessed the β2-Asp/Glu motif.
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Affiliation(s)
- Paola Laurino
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ágnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rubén Meana-Pañeda
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei Lin
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan S. Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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52
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Schaeffer RD, Kinch LN, Liao Y, Grishin NV. Classification of proteins with shared motifs and internal repeats in the ECOD database. Protein Sci 2016; 25:1188-203. [PMID: 26833690 DOI: 10.1002/pro.2893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/23/2016] [Accepted: 01/27/2016] [Indexed: 12/19/2022]
Abstract
Proteins and their domains evolve by a set of events commonly including the duplication and divergence of small motifs. The presence of short repetitive regions in domains has generally constituted a difficult case for structural domain classifications and their hierarchies. We developed the Evolutionary Classification Of protein Domains (ECOD) in part to implement a new schema for the classification of these types of proteins. Here we document the ways in which ECOD classifies proteins with small internal repeats, widespread functional motifs, and assemblies of small domain-like fragments in its evolutionary schema. We illustrate the ways in which the structural genomics project impacted the classification and characterization of new structural domains and sequence families over the decade.
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Affiliation(s)
- R Dustin Schaeffer
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
| | - Yuxing Liao
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
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Liu X, Huang Y, Liang J, Wang J, Shen Y, Li Y, Zhao Y. Characterization of the malaria parasite protein PfTip, a novel invasion-related protein. Mol Med Rep 2016; 13:3303-10. [PMID: 26935027 DOI: 10.3892/mmr.2016.4910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 01/26/2016] [Indexed: 11/06/2022] Open
Abstract
Malaria is one of the most common infective diseases in the world. Invasion of host erythrocytes by the malaria parasite is crucial for pathogen survival and pathogenesis. Various proteins mediate parasite invasion and identification of novel invasion-related proteins may aid in elucidating the underlying molecular mechanism and new intervention strategies for malaria control. This study characterized the PfTip protein, a homolog of the human T‑cell immunomodulatory protein, and examined its function in preventing parasite infection. Bioinformatics analysis and experimental validation were adopted in the present study. Bioinformatics analysis showed that PfTip has a β‑propeller fold in its structure and is highly expressed at the early ring stage. TNFRSF14 was predicted to be a candidate interactant of PfTip. Further analyses showed that PfTip blockage by sera inhibited erythrocyte invasion by the malaria parasite. The protective effect of PfTip was further confirmed through in vivo analysis. To the best of our knowledge, this study is the first to provide evidence on the function of PfTip in erythrocyte parasite invasion. Additional assays involving the receptor of this protein are currently underway.
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Affiliation(s)
- Xuewu Liu
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yuxiao Huang
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jiao Liang
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jun Wang
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yan Shen
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yinghui Li
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Ya Zhao
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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Smock RG, Yadid I, Dym O, Clarke J, Tawfik DS. De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints. Cell 2016; 164:476-86. [PMID: 26806127 PMCID: PMC4735018 DOI: 10.1016/j.cell.2015.12.024] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 10/05/2015] [Accepted: 12/07/2015] [Indexed: 01/02/2023]
Abstract
Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-propeller proteins, a globular and symmetric fold group with diverse functions. The identification of short propeller-like motifs (<50 amino acids) in natural genomes indicated that they expanded via tandem duplications to form extant propellers. We phylogenetically reconstructed 47-residue ancestral motifs that form five-bladed lectin propellers via oligomeric assembly. We demonstrate a functional trajectory of tandem duplications of these motifs leading to monomeric lectins. Foldability, i.e., higher efficiency of folding, was the main parameter leading to improved functionality along the entire evolutionary trajectory. However, folding constraints changed along the trajectory: initially, conflicts between monomer folding and oligomer assembly dominated, whereas subsequently, upon tandem duplication, tradeoffs between monomer stability and foldability took precedence. Inferred 47-aminoacid ancestral motifs fold into functional β-propeller assemblies Motif duplication, fusion, and diversification yield functional monomeric propellers Folding efficiency was the key parameter optimized throughout propeller emergence Single-motif precursors in extant genomes support the reconstructed emergence pathway
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Affiliation(s)
- Robert G Smock
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Itamar Yadid
- Metabolic Pathways and Enzyme Evolution Laboratory, Migal Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Orly Dym
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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Alva V, Söding J, Lupas AN. A vocabulary of ancient peptides at the origin of folded proteins. eLife 2015; 4:e09410. [PMID: 26653858 PMCID: PMC4739770 DOI: 10.7554/elife.09410] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 12/13/2015] [Indexed: 01/01/2023] Open
Abstract
The seemingly limitless diversity of proteins in nature arose from only a few thousand domain prototypes, but the origin of these themselves has remained unclear. We are pursuing the hypothesis that they arose by fusion and accretion from an ancestral set of peptides active as co-factors in RNA-dependent replication and catalysis. Should this be true, contemporary domains may still contain vestiges of such peptides, which could be reconstructed by a comparative approach in the same way in which ancient vocabularies have been reconstructed by the comparative study of modern languages. To test this, we compared domains representative of known folds and identified 40 fragments whose similarity is indicative of common descent, yet which occur in domains currently not thought to be homologous. These fragments are widespread in the most ancient folds and enriched for iron-sulfur- and nucleic acid-binding. We propose that they represent the observable remnants of a primordial RNA-peptide world.
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Affiliation(s)
- Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Johannes Söding
- 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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Ninagawa S, Okada T, Sumitomo Y, Horimoto S, Sugimoto T, Ishikawa T, Takeda S, Yamamoto T, Suzuki T, Kamiya Y, Kato K, Mori K. Forcible destruction of severely misfolded mammalian glycoproteins by the non-glycoprotein ERAD pathway. J Cell Biol 2015; 211:775-84. [PMID: 26572623 PMCID: PMC4657166 DOI: 10.1083/jcb.201504109] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/07/2015] [Indexed: 11/27/2022] Open
Abstract
Higher eukaryotes, but not yeast, are able to extract severely misfolded glycoproteins from the endoplasmic reticulum–associated degradation (ERAD) pathway for glycoproteins and target them to the ERAD pathway for non-glycoproteins to maintain the homeostasis of the ER. Glycoproteins and non-glycoproteins possessing unfolded/misfolded parts in their luminal regions are cleared from the endoplasmic reticulum (ER) by ER-associated degradation (ERAD)-L with distinct mechanisms. Two-step mannose trimming from Man9GlcNAc2 is crucial in the ERAD-L of glycoproteins. We recently showed that this process is initiated by EDEM2 and completed by EDEM3/EDEM1. Here, we constructed chicken and human cells simultaneously deficient in EDEM1/2/3 and analyzed the fates of four ERAD-L substrates containing three potential N-glycosylation sites. We found that native but unstable or somewhat unfolded glycoproteins, such as ATF6α, ATF6α(C), CD3-δ–ΔTM, and EMC1, were stabilized in EDEM1/2/3 triple knockout cells. In marked contrast, degradation of severely misfolded glycoproteins, such as null Hong Kong (NHK) and deletion or insertion mutants of ATF6α(C), CD3-δ–ΔTM, and EMC1, was delayed only at early chase periods, but they were eventually degraded as in wild-type cells. Thus, higher eukaryotes are able to extract severely misfolded glycoproteins from glycoprotein ERAD and target them to the non-glycoprotein ERAD pathway to maintain the homeostasis of the ER.
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Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan
| | - Tetsuya Okada
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshiki Sumitomo
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Horimoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takehiro Sugimoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tokiro Ishikawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan
| | - Yukiko Kamiya
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan
| | - Koichi Kato
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Nikonorova N, Vu LD, Czyzewicz N, Gevaert K, De Smet I. A phylogenetic approach to study the origin and evolution of the CRINKLY4 family. FRONTIERS IN PLANT SCIENCE 2015; 6:880. [PMID: 26557128 PMCID: PMC4617170 DOI: 10.3389/fpls.2015.00880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/02/2015] [Indexed: 05/03/2023]
Abstract
Cell-cell communication plays a crucial role in plant growth and development and relies to a large extent on peptide ligand-receptor kinase signaling mechanisms. The CRINKLY4 (CR4) family of receptor-like kinases is involved in a wide range of developmental processes in plants, including mediating columella stem cell identity and differentiation in the Arabidopsis thaliana root tip. Members of the CR4 family contain a signal peptide, an extracellular part, a single-pass transmembrane helix and an intracellular cytoplasmic protein kinase domain. The main distinguishing features of the family are the presence of seven "crinkly" repeats and a TUMOR NECROSIS FACTOR RECEPTOR (TNFR)-like domain in the extracellular part. Here, we investigated the evolutionary origin of the CR4 family and explored to what extent members of this family are conserved throughout the green lineage. We identified members of the CR4 family in various dicots and monocots, and also in the lycophyte Selaginella moellendorffii and the bryophyte Physcomitrella patens. In addition, we attempted to gain insight in the evolutionary origin of different CR4-specific domains, and we could detect "crinkly" repeat containing proteins already in single celled algae. Finally, we related the presence of likely functional CR4 orthologs to its best described signaling module comprising CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 40 (CLE40), WUSCHEL RELATED HOMEOBOX 5 (WOX5), CLAVATA 1 (CLV1), and ARABIDOPSIS CR4 (ACR4), and established that this module likely is already present in bryophytes and lycophytes.
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Affiliation(s)
- Natalia Nikonorova
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB)Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Lam D. Vu
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB)Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Department of Medical Protein Research, Flanders Institute for Biotechnology (VIB), Ghent UniversityGhent, Belgium
- Department of Biochemistry, Ghent UniversityGhent, Belgium
| | - Nathan Czyzewicz
- Division of Plant and Crop Sciences, School of Biosciences, University of NottinghamLoughborough, UK
| | - Kris Gevaert
- Department of Medical Protein Research, Flanders Institute for Biotechnology (VIB), Ghent UniversityGhent, Belgium
- Department of Biochemistry, Ghent UniversityGhent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB)Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Division of Plant and Crop Sciences, School of Biosciences, University of NottinghamLoughborough, UK
- Center for Plant Integrative Biology, University of NottinghamLoughborough, UK
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58
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De novo protein design: how do we expand into the universe of possible protein structures? Curr Opin Struct Biol 2015; 33:16-26. [DOI: 10.1016/j.sbi.2015.05.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/15/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
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59
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Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY. Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol Direct 2015. [PMID: 26014357 DOI: 10.1186/s13062-015-0059- 4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure. RESULTS We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical. CONCLUSIONS The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis.
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Affiliation(s)
- Daria N Shalaeva
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia.
| | - Daria V Dibrova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA.
| | - Armen Y Mulkidjanian
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia. .,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
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60
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Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY. Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol Direct 2015; 10:29. [PMID: 26014357 PMCID: PMC4445527 DOI: 10.1186/s13062-015-0059-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 05/13/2015] [Indexed: 12/19/2022] Open
Abstract
Background Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure. Results We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical. Conclusions The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis. Reviewers This article was reviewed by Andrei L. Osterman, Narayanaswamy Srinivasan, Igor N. Berezovsky, and Gerrit Vriend (nominated by Martijn Huynen). Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0059-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria N Shalaeva
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia.
| | - Daria V Dibrova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA.
| | - Armen Y Mulkidjanian
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia. .,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
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61
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Naeem ul Hassan M, Zainal Z, Ismail I. Plant kelch containing F-box proteins: structure, evolution and functions. RSC Adv 2015. [DOI: 10.1039/c5ra01875g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Kelch repeat containing F-box proteins; a review on the progress of the research on these plant specific signalling proteins.
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Affiliation(s)
- M. Naeem ul Hassan
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Bangi, 43600
- Malaysia
| | - Zamri Zainal
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Bangi, 43600
- Malaysia
| | - Ismanizan Ismail
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Bangi, 43600
- Malaysia
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62
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Thomson AR, Wood CW, Burton AJ, Bartlett GJ, Sessions RB, Brady RL, Woolfson DN. Computational design of water-soluble α-helical barrels. Science 2014; 346:485-8. [DOI: 10.1126/science.1257452] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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63
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Voet ARD, Noguchi H, Addy C, Simoncini D, Terada D, Unzai S, Park SY, Zhang KYJ, Tame JRH. Computational design of a self-assembling symmetrical β-propeller protein. Proc Natl Acad Sci U S A 2014; 111:15102-7. [PMID: 25288768 PMCID: PMC4210308 DOI: 10.1073/pnas.1412768111] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The modular structure of many protein families, such as β-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical β-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.
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Affiliation(s)
- Arnout R D Voet
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; and Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Noguchi
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Christine Addy
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - David Simoncini
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; and
| | - Daiki Terada
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Satoru Unzai
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Sam-Yong Park
- Drug Design Laboratory, 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, Yokohama, Kanagawa 230-0045, Japan; and
| | - 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
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64
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Evolutionary relationship of two ancient protein superfolds. Nat Chem Biol 2014; 10:710-5. [PMID: 25038785 DOI: 10.1038/nchembio.1579] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/02/2014] [Indexed: 01/29/2023]
Abstract
Proteins are the molecular machines of the cell that fold into specific three-dimensional structures to fulfill their functions. To improve our understanding of how the structure and function of proteins arises, it is crucial to understand how evolution has generated the structural diversity we observe today. Classically, proteins that adopt different folds are considered to be nonhomologous. However, using state-of-the-art tools for homology detection, we found evidence of homology between proteins of two ancient and highly populated protein folds, the (βα)8-barrel and the flavodoxin-like fold. We detected a family of sequences that show intermediate features between both folds and determined what is to our knowledge the first representative crystal structure of one of its members, giving new insights into the evolutionary link of two of the earliest folds. Our findings contribute to an emergent vision where protein superfolds share common ancestry and encourage further approaches to complete the mapping of structure space onto sequence space.
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65
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Höcker B. Design of proteins from smaller fragments-learning from evolution. Curr Opin Struct Biol 2014; 27:56-62. [PMID: 24865156 DOI: 10.1016/j.sbi.2014.04.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
Nature has generated an impressive set of proteins with diverse folds and functions. It has been able to do so using mechanisms such as duplication and fusion as well as recombination of smaller protein fragments that serve as building blocks. These evolutionary mechanisms provide a template for the rational design of new proteins from fragments of existing proteins. Design by duplication and fusion has been explored for a number of symmetric protein folds, while design by rational recombination has just emerged. First experiments in recombining fragments from the same and different folds are proving successful in building new proteins that harbor easily evolvable properties originating from the parents. Overall, duplication and recombination of smaller fragments shows much potential for future applications in the design of proteins.
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Affiliation(s)
- Birte Höcker
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany.
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