1
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Ramprasad S, Nyarko A. Ensembles of interconverting protein complexes with multiple interaction domains. Curr Opin Struct Biol 2024; 88:102874. [PMID: 38981144 DOI: 10.1016/j.sbi.2024.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Many critical biological processes depend on protein complexes that exist as ensembles of subcomplexes rather than a discrete complex. The subcomplexes dynamically interconvert with one another, and the ability to accurately resolve the composition of the diverse molecular species in the ensemble is crucial for understanding the contribution of each subcomplex to the overall function of the protein complex. Advances in computational programs have made it possible to predict the various molecular species in these ensembles, but experimental approaches to identify the pool of subcomplexes and associated stoichiometries are often challenging. This review highlights some experimental approaches that can be used to resolve the diverse molecular species in protein complexes that exist as ensembles of sub complexes.
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Affiliation(s)
- Sanjay Ramprasad
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Afua Nyarko
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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2
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Vosseberg J, van Hooff JJE, Köstlbacher S, Panagiotou K, Tamarit D, Ettema TJG. The emerging view on the origin and early evolution of eukaryotic cells. Nature 2024; 633:295-305. [PMID: 39261613 DOI: 10.1038/s41586-024-07677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/05/2024] [Indexed: 09/13/2024]
Abstract
The origin of the eukaryotic cell, with its compartmentalized nature and generally large size compared with bacterial and archaeal cells, represents a cornerstone event in the evolution of complex life on Earth. In a process referred to as eukaryogenesis, the eukaryotic cell is believed to have evolved between approximately 1.8 and 2.7 billion years ago from its archaeal ancestors, with a symbiosis with a bacterial (proto-mitochondrial) partner being a key event. In the tree of life, the branch separating the first from the last common ancestor of all eukaryotes is long and lacks evolutionary intermediates. As a result, the timing and driving forces of the emergence of complex eukaryotic features remain poorly understood. During the past decade, environmental and comparative genomic studies have revealed vital details about the identity and nature of the host cell and the proto-mitochondrial endosymbiont, enabling a critical reappraisal of hypotheses underlying the symbiotic origin of the eukaryotic cell. Here we outline our current understanding of the key players and events underlying the emergence of cellular complexity during the prokaryote-to-eukaryote transition and discuss potential avenues of future research that might provide new insights into the enigmatic origin of the eukaryotic cell.
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Affiliation(s)
- Julian Vosseberg
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jolien J E van Hooff
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kassiani Panagiotou
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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3
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Munaron L, Chinigò G, Scarpellino G, Ruffinatti FA. The fallacy of functional nomenclature in the kingdom of biological multifunctionality: physiological and evolutionary considerations on ion channels. J Physiol 2024; 602:2367-2381. [PMID: 37635695 DOI: 10.1113/jp284422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Living organisms are multiscale complex systems that have evolved high degrees of multifunctionality and redundancy in the structure-function relationship. A number of factors, only in part determined genetically, affect the jobs of proteins. The overall structural organization confers unique molecular properties that provide the potential to perform a pattern of activities, some of which are co-opted by specific environments. The variety of multifunctional proteins is expanding, but most cases are handled individually and according to the still dominant 'one structure-one function' approach, which relies on the attribution of canonical names typically referring to the first task identified for a given protein. The present topical review focuses on the multifunctionality of ion channels as a paradigmatic example. Mounting evidence reports the ability of many ion channels (including members of voltage-dependent, ligand-gated and transient receptor potential families) to exert biological effects independently of their ion conductivity. 'Functionally based' nomenclature (the practice of naming a protein or family of proteins based on a single purpose) is a conceptual bias for three main reasons: (i) it increases the amount of ambiguity, deceiving our understanding of the multiple contributions of biomolecules that is the heart of the complexity; (ii) it is in stark contrast to protein evolution dynamics, largely based on multidomain arrangement; and (iii) it overlooks the crucial role played by the microenvironment in adjusting the actions of cell structures and in tuning protein isoform diversity to accomplish adaptational requirements. Biological information in protein physiology is distributed among different entwined layers working as the primary 'locus' of natural selection and of evolutionary constraints.
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Affiliation(s)
- Luca Munaron
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Chinigò
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Scarpellino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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4
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Žoldák G, Knappe TA, Geitner AJ, Scholz C, Dobbek H, Schmid FX, Jakob RP. Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis. Molecules 2024; 29:1440. [PMID: 38611720 PMCID: PMC11013033 DOI: 10.3390/molecules29071440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.
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Affiliation(s)
- Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
| | - Thomas A. Knappe
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | | | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Roman P. Jakob
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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5
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García-Paz FDM, Del Moral S, Morales-Arrieta S, Ayala M, Treviño-Quintanilla LG, Olvera-Carranza C. Multidomain chimeric enzymes as a promising alternative for biocatalysts improvement: a minireview. Mol Biol Rep 2024; 51:410. [PMID: 38466518 DOI: 10.1007/s11033-024-09332-9] [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: 10/26/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.
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Affiliation(s)
- Flor de María García-Paz
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México
| | - Sandra Del Moral
- Investigador por México-CONAHCyT, Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México, Campus Veracruz. MA de Quevedo 2779, Col. Formando Hogar, CP 91960, Veracruz, Veracruz, México
| | - Sandra Morales-Arrieta
- Departamento de Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566 Col. Lomas del Texcal CP 62550, Jiutepec, Morelos, México
| | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México
| | - Luis Gerardo Treviño-Quintanilla
- Departamento de Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566 Col. Lomas del Texcal CP 62550, Jiutepec, Morelos, México
| | - Clarita Olvera-Carranza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México.
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6
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Kannan A, Chaurasiya DK, Naganathan AN. Conflicting Interfacial Electrostatic Interactions as a Design Principle to Modulate Long-Range Interdomain Communication. ACS BIO & MED CHEM AU 2024; 4:53-67. [PMID: 38404745 PMCID: PMC10885104 DOI: 10.1021/acsbiomedchemau.3c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 02/27/2024]
Abstract
The extent and molecular basis of interdomain communication in multidomain proteins, central to understanding allostery and function, is an open question. One simple evolutionary strategy could involve the selection of either conflicting or favorable electrostatic interactions across the interface of two closely spaced domains to tune the magnitude of interdomain connectivity. Here, we study a bilobed domain FF34 from the eukaryotic p190A RhoGAP protein to explore one such design principle that mediates interdomain communication. We find that while the individual structural units in wild-type FF34 are marginally coupled, they exhibit distinct intrinsic stabilities and low cooperativity, manifesting as slow folding. The FF3-FF4 interface harbors a frustrated network of highly conserved electrostatic interactions-a charge troika-that promotes the population of multiple, decoupled, and non-native structural modes on a rugged native landscape. Perturbing this network via a charge-reversal mutation not only enhances stability and cooperativity but also dampens the fluctuations globally and speeds up the folding rate by at least an order of magnitude. Our work highlights how a conserved but nonoptimal network of interfacial electrostatic interactions shapes the native ensemble of a bilobed protein, a feature that could be exploited in designing molecular systems with long-range connectivity and enhanced cooperativity.
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Affiliation(s)
- Adithi Kannan
- Department of Biotechnology,
Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology,
Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology,
Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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7
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Kruglikov A, Xia X. Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria. Int J Mol Sci 2024; 25:2000. [PMID: 38396678 PMCID: PMC10889376 DOI: 10.3390/ijms25042000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The dynamic structures and varying functions of intrinsically disordered proteins (IDPs) have made them fascinating subjects in molecular biology. Investigating IDP abundance in different bacterial species is crucial for understanding adaptive strategies in diverse environments. Notably, thermophilic bacteria have lower IDP abundance than mesophiles, and a negative correlation with optimal growth temperature (OGT) has been observed. However, the factors driving these trends are yet to be fully understood. We examined the types of IDPs present in both mesophiles and thermophiles alongside those unique to just mesophiles. The shared group of IDPs exhibits similar disorder levels in the two groups of species, suggesting that certain IDPs unique to mesophiles may contribute to the observed decrease in IDP abundance as OGT increases. Subsequently, we used quasi-independent contrasts to explore the relationship between OGT and IDP abundance evolution. Interestingly, we found no significant relationship between OGT and IDP abundance contrasts, suggesting that the evolution of lower IDP abundance in thermophiles may not be solely linked to OGT. This study provides a foundation for future research into the intricate relationship between IDP evolution and environmental adaptation. Our findings support further research on the adaptive significance of intrinsic disorder in bacterial species.
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Affiliation(s)
- Alibek Kruglikov
- Department of Biology, University of Ottawa, 30 Marie Curie, Station A, P.O. Box 450, Ottawa, ON K1N 6N5, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Station A, P.O. Box 450, Ottawa, ON K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
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8
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Gollapalli P, Rudrappa S, Kumar V, Santosh Kumar HS. Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery. J Mol Evol 2023; 91:598-615. [PMID: 37626222 DOI: 10.1007/s00239-023-10129-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Genes duplicate, mutate, recombine, fuse or fission to produce new genes, or when genes are formed from de novo, novel functions arise during evolution. Researchers have tried to quantify the causes of these molecular diversification processes to know how these genes increase molecular complexity over a period of time, for instance protein domain organization. In contrast to global sequence similarity, protein domain architectures can capture key structural and functional characteristics, making them better proxies for describing functional equivalence. In Prokaryotes and eukaryotes it has proven that, domain designs are retained over significant evolutionary distances. Protein domain architectures are now being utilized to categorize and distinguish evolutionarily related proteins and find homologs among species that are evolutionarily distant from one another. Additionally, structural information stored in domain structures has accelerated homology identification and sequence search methods. Tools for functional protein annotation have been developed to discover, protein domain content, domain order, domain recurrence, and domain position as all these contribute to the prediction of protein functional accuracy. In this review, an attempt is made to summarise facts and speculations regarding the use of protein domain architecture and modularity to identify possible therapeutic targets among cellular activities based on the understanding their linked biological processes.
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Affiliation(s)
- Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Sushmitha Rudrappa
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka, 577451, India
| | - Vadlapudi Kumar
- Department of Biochemistry, Davangere University, Shivagangothri, Davangere, Karnataka, 577007, India
| | - Hulikal Shivashankara Santosh Kumar
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka, 577451, India.
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9
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Deryusheva EI, Machulin AV, Galzitskaya OV. Diversity and features of proteins with structural repeats. Biophys Rev 2023; 15:1159-1169. [PMID: 37974986 PMCID: PMC10643770 DOI: 10.1007/s12551-023-01130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 11/19/2023] Open
Abstract
The review provides information on proteins with structural repeats, including their classification, characteristics, functions, and relevance in disease development. It explores methods for identifying structural repeats and specialized databases. The review also highlights the potential use of repeat proteins as drug design scaffolds and discusses their evolutionary mechanisms.
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Affiliation(s)
- Evgeniya I. Deryusheva
- Institute for Biological Instrumentation, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Andrey V. Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences, Pushchino, Russia
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10
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Gizak A. Multitasking Proteins and Their Involvement in Pathogenesis. Cells 2023; 12:1460. [PMID: 37296581 PMCID: PMC10253090 DOI: 10.3390/cells12111460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The "one protein, one function" paradigm, similar to the "one gene, one enzyme" hypothesis that dominated our thinking for a long time, has proven to be too simplistic [...].
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Affiliation(s)
- Agnieszka Gizak
- Department of Molecular Physiology and Neurobiology, University of Wrocław, ul. Sienkiewicza 21, 50-335 Wroclaw, Poland
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11
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Carss KJ, Deaton AM, Del Rio-Espinola A, Diogo D, Fielden M, Kulkarni DA, Moggs J, Newham P, Nelson MR, Sistare FD, Ward LD, Yuan J. Using human genetics to improve safety assessment of therapeutics. Nat Rev Drug Discov 2023; 22:145-162. [PMID: 36261593 DOI: 10.1038/s41573-022-00561-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.
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Affiliation(s)
| | - Aimee M Deaton
- Amgen, Cambridge, MA, USA.,Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Alberto Del Rio-Espinola
- Novartis Institutes for BioMedical Research, Basel, Switzerland.,GentiBio Inc., Cambridge, MA, USA
| | | | - Mark Fielden
- Amgen, Thousand Oaks, MA, USA.,Kate Therapeutics, San Diego, CA, USA
| | | | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Frank D Sistare
- Merck & Co., West Point, PA, USA.,315 Meadowmont Ln, Chapel Hill, NC, USA
| | - Lucas D Ward
- Amgen, Cambridge, MA, USA. .,Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Jing Yuan
- Amgen, Cambridge, MA, USA.,Pfizer, Cambridge, MA, USA
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12
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The Modular Architecture of Metallothioneins Facilitates Domain Rearrangements and Contributes to Their Evolvability in Metal-Accumulating Mollusks. Int J Mol Sci 2022; 23:ijms232415824. [PMID: 36555472 PMCID: PMC9781358 DOI: 10.3390/ijms232415824] [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: 11/10/2022] [Revised: 12/05/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Protein domains are independent structural and functional modules that can rearrange to create new proteins. While the evolution of multidomain proteins through the shuffling of different preexisting domains has been well documented, the evolution of domain repeat proteins and the origin of new domains are less understood. Metallothioneins (MTs) provide a good case study considering that they consist of metal-binding domain repeats, some of them with a likely de novo origin. In mollusks, for instance, most MTs are bidomain proteins that arose by lineage-specific rearrangements between six putative domains: α, β1, β2, β3, γ and δ. Some domains have been characterized in bivalves and gastropods, but nothing is known about the MTs and their domains of other Mollusca classes. To fill this gap, we investigated the metal-binding features of NpoMT1 of Nautilus pompilius (Cephalopoda class) and FcaMT1 of Falcidens caudatus (Caudofoveata class). Interestingly, whereas NpoMT1 consists of α and β1 domains and has a prototypical Cd2+ preference, FcaMT1 has a singular preference for Zn2+ ions and a distinct domain composition, including a new Caudofoveata-specific δ domain. Overall, our results suggest that the modular architecture of MTs has contributed to MT evolution during mollusk diversification, and exemplify how modularity increases MT evolvability.
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13
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Goult BT, von Essen M, Hytönen VP. The mechanical cell - the role of force dependencies in synchronising protein interaction networks. J Cell Sci 2022; 135:283155. [PMID: 36398718 PMCID: PMC9845749 DOI: 10.1242/jcs.259769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The role of mechanical signals in the proper functioning of organisms is increasingly recognised, and every cell senses physical forces and responds to them. These forces are generated both from outside the cell or via the sophisticated force-generation machinery of the cell, the cytoskeleton. All regions of the cell are connected via mechanical linkages, enabling the whole cell to function as a mechanical system. In this Review, we define some of the key concepts of how this machinery functions, highlighting the critical requirement for mechanosensory proteins, and conceptualise the coupling of mechanical linkages to mechanochemical switches that enables forces to be converted into biological signals. These mechanical couplings provide a mechanism for how mechanical crosstalk might coordinate the entire cell, its neighbours, extending into whole collections of cells, in tissues and in organs, and ultimately in the coordination and operation of entire organisms. Consequently, many diseases manifest through defects in this machinery, which we map onto schematics of the mechanical linkages within a cell. This mapping approach paves the way for the identification of additional linkages between mechanosignalling pathways and so might identify treatments for diseases, where mechanical connections are affected by mutations or where individual force-regulated components are defective.
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Affiliation(s)
- Benjamin T. Goult
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK,Authors for correspondence (; )
| | - Magdaléna von Essen
- Faculty of Medicine and Health Technology, Tampere University, FI-33100 Tampere, Finland
| | - Vesa P. Hytönen
- Faculty of Medicine and Health Technology, Tampere University, FI-33100 Tampere, Finland,Fimlab Laboratories, FI-33520 Tampere, Finland,Authors for correspondence (; )
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14
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Exploring the effect of tethered domains on the folding of Grb2 protein. Arch Biochem Biophys 2022; 731:109444. [DOI: 10.1016/j.abb.2022.109444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022]
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15
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Hamilton GL, Saikia N, Basak S, Welcome FS, Wu F, Kubiak J, Zhang C, Hao Y, Seidel CAM, Ding F, Sanabria H, Bowen ME. Fuzzy supertertiary interactions within PSD-95 enable ligand binding. eLife 2022; 11:e77242. [PMID: 36069777 PMCID: PMC9581536 DOI: 10.7554/elife.77242] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
The scaffold protein PSD-95 links postsynaptic receptors to sites of presynaptic neurotransmitter release. Flexible linkers between folded domains in PSD-95 enable a dynamic supertertiary structure. Interdomain interactions within the PSG supramodule, formed by PDZ3, SH3, and Guanylate Kinase domains, regulate PSD-95 activity. Here we combined discrete molecular dynamics and single molecule Förster resonance energy transfer (FRET) to characterize the PSG supramodule, with time resolution spanning picoseconds to seconds. We used a FRET network to measure distances in full-length PSD-95 and model the conformational ensemble. We found that PDZ3 samples two conformational basins, which we confirmed with disulfide mapping. To understand effects on activity, we measured binding of the synaptic adhesion protein neuroligin. We found that PSD-95 bound neuroligin well at physiological pH while truncated PDZ3 bound poorly. Our hybrid structural models reveal how the supertertiary context of PDZ3 enables recognition of this critical synaptic ligand.
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Affiliation(s)
- George L Hamilton
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Nabanita Saikia
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Sujit Basak
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Franceine S Welcome
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Fang Wu
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Jakub Kubiak
- Molecular Physical Chemistry, Heinrich Heine UniversityDüsseldorfGermany
| | - Changcheng Zhang
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Yan Hao
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Claus AM Seidel
- Molecular Physical Chemistry, Heinrich Heine UniversityDüsseldorfGermany
| | - Feng Ding
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
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16
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Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochem Soc Trans 2022; 50:541-554. [PMID: 35129612 DOI: 10.1042/bst20210499] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
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17
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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18
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Hirn M, Little A. Wavelet invariants for statistically robust multi-reference alignment. INFORMATION AND INFERENCE : A JOURNAL OF THE IMA 2021; 10:1287-1351. [PMID: 35070296 PMCID: PMC8782248 DOI: 10.1093/imaiai/iaaa016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We propose a nonlinear, wavelet-based signal representation that is translation invariant and robust to both additive noise and random dilations. Motivated by the multi-reference alignment problem and generalizations thereof, we analyze the statistical properties of this representation given a large number of independent corruptions of a target signal. We prove the nonlinear wavelet-based representation uniquely defines the power spectrum but allows for an unbiasing procedure that cannot be directly applied to the power spectrum. After unbiasing the representation to remove the effects of the additive noise and random dilations, we recover an approximation of the power spectrum by solving a convex optimization problem, and thus reduce to a phase retrieval problem. Extensive numerical experiments demonstrate the statistical robustness of this approximation procedure.
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Affiliation(s)
- Matthew Hirn
- Department of Computational Mathematics, Science and Engineering, Department of Mathematics and Center for Quantum Computing, Science and Engineering, Michigan State University, East Lansing, MI 48824
| | - Anna Little
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824
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19
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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20
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Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Mulnaes D, Golchin P, Koenig F, Gohlke H. TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning. J Chem Theory Comput 2021; 17:4599-4613. [PMID: 34161735 DOI: 10.1021/acs.jctc.1c00129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. Current domain boundary prediction methods differ in terms of boundary definition, methodology, and training databases resulting in disparate performance for different proteins. We developed TopDomain, an exhaustive metapredictor, that uses deep neural networks to combine multisource information from sequence- and homology-based features of over 50 primary predictors. For this purpose, we developed a new domain boundary data set termed the TopDomain data set, in which the true annotations are informed by SCOPe annotations, structural domain parsers, human inspection, and deep learning. We benchmark TopDomain against 2484 targets with 3354 boundaries from the TopDomain test set and achieve F1 scores of 78.4% and 73.8% for multidomain boundary prediction within ±20 residues and ±10 residues of the true boundary, respectively. When examined on targets from CASP11-13 competitions, TopDomain achieves F1 scores of 47.5% and 42.8% for multidomain proteins. TopDomain significantly outperforms 15 widely used, state-of-the-art ab initio and homology-based domain boundary predictors. Finally, we implemented TopDomainTMC, which accurately predicts whether domain parsing is necessary for the target protein.
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Affiliation(s)
- Daniel Mulnaes
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Pegah Golchin
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Filip Koenig
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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22
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Yamaguchi H, Saito Y. Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins. Brief Bioinform 2021; 22:6309928. [PMID: 34180966 DOI: 10.1093/bib/bbab234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 12/14/2022] Open
Abstract
Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However, it is unclear how to effectively learn evolutionary properties of an engineering target protein from homologous sequences, taking into account the protein's sequence-level structure called domain architecture (DA). Additionally, no optimal protocols are established for incorporating such properties into Transformer, the neural network well-known to perform the best in natural language processing research. This article proposes DA-aware evolutionary fine-tuning, or 'evotuning', protocols for Transformer-based variant effect prediction, considering various combinations of homology search, fine-tuning and sequence vectorization strategies. We exhaustively evaluated our protocols on diverse proteins with different functions and DAs. The results indicated that our protocols achieved significantly better performances than previous DA-unaware ones. The visualizations of attention maps suggested that the structural information was incorporated by evotuning without direct supervision, possibly leading to better prediction accuracy.
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Affiliation(s)
- Hideki Yamaguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Yutaka Saito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan.,AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Shinjuku-ku, Tokyo 169-8555, Japan
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23
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Queirós P, Delogu F, Hickl O, May P, Wilmes P. Mantis: flexible and consensus-driven genome annotation. Gigascience 2021; 10:6291114. [PMID: 34076241 PMCID: PMC8170692 DOI: 10.1093/gigascience/giab042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/22/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
Background The rapid development of the (meta-)omics fields has produced an unprecedented amount of high-resolution and high-fidelity data. Through the use of these datasets we can infer the role of previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation can be described as the identification of regions of interest (i.e., domains) in protein sequences and the assignment of biological functions. Despite the existence of numerous tools, challenges remain in terms of speed, flexibility, and reproducibility. In the big data era, it is also increasingly important to cease limiting our findings to a single reference, coalescing knowledge from different data sources, and thus overcoming some limitations in overly relying on computationally generated data from single sources. Results We implemented a protein annotation tool, Mantis, which uses database identifiers intersection and text mining to integrate knowledge from multiple reference data sources into a single consensus-driven output. Mantis is flexible, allowing for the customization of reference data and execution parameters, and is reproducible across different research goals and user environments. We implemented a depth-first search algorithm for domain-specific annotation, which significantly improved annotation performance compared to sequence-wide annotation. The parallelized implementation of Mantis results in short runtimes while also outputting high coverage and high-quality protein function annotations. Conclusions Mantis is a protein function annotation tool that produces high-quality consensus-driven protein annotations. It is easy to set up, customize, and use, scaling from single genomes to large metagenomes. Mantis is available under the MIT license at https://github.com/PedroMTQ/mantis.
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Affiliation(s)
- Pedro Queirós
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367 Esch-sur-Alzette, Luxembourg
| | - Francesco Delogu
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367 Esch-sur-Alzette, Luxembourg
| | - Oskar Hickl
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367 Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367 Esch-sur-Alzette, Luxembourg
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24
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Schaller KS, Kari J, Molina GA, Tidemand KD, Borch K, Peters GHJ, Westh P. Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach. ACS OMEGA 2021; 6:1547-1555. [PMID: 33490814 PMCID: PMC7818601 DOI: 10.1021/acsomega.0c05361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/24/2020] [Indexed: 05/21/2023]
Abstract
While heterogeneous enzyme reactions play an essential role in both nature and green industries, computational predictions of their catalytic properties remain scarce. Recent experimental work demonstrated the applicability of the Sabatier principle for heterogeneous biocatalysis. This provides a simple relationship between binding strength and the catalytic rate and potentially opens a new way for inexpensive computational determination of kinetic parameters. However, broader implementation of this approach will require fast and reliable prediction of binding free energies of complex two-phase systems, and computational procedures for this are still elusive. Here, we propose a new framework for the assessment of the binding strengths of multidomain proteins, in general, and interfacial enzymes, in particular, based on an extended linear interaction energy (LIE) method. This two-domain LIE (2D-LIE) approach was successfully applied to predict binding and activation free energies of a diverse set of cellulases and resulted in robust models with high accuracy. Overall, our method provides a fast computational screening tool for cellulases that have not been experimentally characterized, and we posit that it may also be applicable to other heterogeneously acting biocatalysts.
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Affiliation(s)
- Kay S. Schaller
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Gustavo A. Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes
A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- . Phone: +45 45 25 26 41
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25
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Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020; 9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023] Open
Abstract
The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
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26
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Czubat B, Minias A, Brzostek A, Żaczek A, Struś K, Zakrzewska-Czerwińska J, Dziadek J. Functional Disassociation Between the Protein Domains of MSMEG_4305 of Mycolicibacterium smegmatis ( Mycobacterium smegmatis) in vivo. Front Microbiol 2020; 11:2008. [PMID: 32973726 PMCID: PMC7466739 DOI: 10.3389/fmicb.2020.02008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/29/2020] [Indexed: 12/02/2022] Open
Abstract
MSMEG_4305 is a two-domain protein of Mycolicibacterium smegmatis (Mycobacterium smegmatis) (Mycolicibacterium smegmatis). The N-terminal domain of MSMEG_4305 encodes an RNase H type I. The C-terminal domain is a presumed CobC, predicted to be involved in the aerobic synthesis of vitamin B12. Both domains reach their maximum at distinct pH, approximately 8.5 and 4.5, respectively. The presence of the CobC domain influenced RNase activity in vitro in homolog Rv2228c. Here, we analyzed the role of MSMEG_4305 in vitamin B12 synthesis and the functional association between both domains in vivo in M. smegmatis. We used knock-out mutant of M. smegmatis, deficient in MSMEG_4305. Whole-cell lysates of the mutants strain contained a lower concentration of vitamin B12, as it determined with immunoenzimatic assay. We observed growth deficits, related to vitamin B12 production, on media containing sulfamethazine and propionate. Removal of the CobC domain of MSMEG_4305 in ΔrnhA background hardly affected the growth rate of M. smegmatis in vivo. The strain carrying truncation showed no fitness deficit in the competitive assay and it did not show increased level of RNA/DNA hybrids in its genome. We show that homologs of MSMEG_4305 are present only in the Actinomycetales phylogenetic branch (according to the old classification system). The domains of MSMEG_4305 homologs accumulate mutations at a different rate, while the linker region is highly variable. We conclude that MSMEG_4305 is a multidomain protein that most probably was fixed in the phylogenetic tree of life due to genetic drift.
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Affiliation(s)
- Bożena Czubat
- Department of Experimental and Clinical Pharmacology, University of Rzeszów, Rzeszów, Poland.,Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Anna Brzostek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Anna Żaczek
- Institute of Medical Sciences, Medical College of Rzeszów University, Rzeszów, Poland
| | - Katarzyna Struś
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszów, Rzeszów, Poland
| | | | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
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27
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Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning. J Mol Biol 2020; 432:4435-4446. [PMID: 32485208 DOI: 10.1016/j.jmb.2020.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/06/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022]
Abstract
How protein domain structure changes in response to mutations is not well understood. Some mutations change the structure drastically, while most only result in small changes. To gain an understanding of this, we decompose the relationship between changes in domain sequence and structure using machine learning. We select pairs of evolutionarily related domains with a broad range of evolutionary distances. In contrast to earlier studies, we do not find a strictly linear relationship between sequence and structural changes. We train a random forest regressor that predicts the structural similarity between pairs with an average accuracy of 0.029 lDDT ( local Distance Difference Test) score, and a correlation coefficient of 0.92. Decomposing the feature importance shows that the domain length, or analogously, size is the most important feature. Our model enables assessing deviations in relative structural response, and thus prediction of evolutionary trajectories, in protein domains across evolution.
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28
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Narykov O, Bogatov D, Korkin D. DISPOT: a simple knowledge-based protein domain interaction statistical potential. Bioinformatics 2020; 35:5374-5378. [PMID: 31350874 PMCID: PMC6954640 DOI: 10.1093/bioinformatics/btz587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 06/17/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION The complexity of protein-protein interactions (PPIs) is further compounded by the fact that an average protein consists of two or more domains, structurally and evolutionary independent subunits. Experimental studies have demonstrated that an interaction between a pair of proteins is not carried out by all domains constituting each protein, but rather by a select subset. However, determining which domains from each protein mediate the corresponding PPI is a challenging task. RESULTS Here, we present domain interaction statistical potential (DISPOT), a simple knowledge-based statistical potential that estimates the propensity of an interaction between a pair of protein domains, given their structural classification of protein (SCOP) family annotations. The statistical potential is derived based on the analysis of >352 000 structurally resolved PPIs obtained from DOMMINO, a comprehensive database of structurally resolved macromolecular interactions. AVAILABILITY AND IMPLEMENTATION DISPOT is implemented in Python 2.7 and packaged as an open-source tool. DISPOT is implemented in two modes, basic and auto-extraction. The source code for both modes is available on GitHub: https://github.com/korkinlab/dispot and standalone docker images on DockerHub: https://hub.docker.com/r/korkinlab/dispot. The web server is freely available at http://dispot.korkinlab.org/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Oleksandr Narykov
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Dmytro Bogatov
- Department of Computer Science, Boston University, Boston, MA, USA
| | - Dmitry Korkin
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA, USA.,Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
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29
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Espinosa-Cantú A, Cruz-Bonilla E, Noda-Garcia L, DeLuna A. Multiple Forms of Multifunctional Proteins in Health and Disease. Front Cell Dev Biol 2020; 8:451. [PMID: 32587857 PMCID: PMC7297953 DOI: 10.3389/fcell.2020.00451] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/14/2020] [Indexed: 12/23/2022] Open
Abstract
Protein science has moved from a focus on individual molecules to an integrated perspective in which proteins emerge as dynamic players with multiple functions, rather than monofunctional specialists. Annotation of the full functional repertoire of proteins has impacted the fields of biochemistry and genetics, and will continue to influence basic and applied science questions - from the genotype-to-phenotype problem, to our understanding of human pathologies and drug design. In this review, we address the phenomena of pleiotropy, multidomain proteins, promiscuity, and protein moonlighting, providing examples of multitasking biomolecules that underlie specific mechanisms of human disease. In doing so, we place in context different types of multifunctional proteins, highlighting useful attributes for their systematic definition and classification in future research directions.
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Affiliation(s)
- Adriana Espinosa-Cantú
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Guanajuato, Mexico
| | - Erika Cruz-Bonilla
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Guanajuato, Mexico
| | - Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Guanajuato, Mexico
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30
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Matsuno S, Ohue M, Akiyama Y. Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces. Biophys Physicobiol 2020; 17:2-13. [PMID: 32509489 PMCID: PMC7246089 DOI: 10.2142/biophysico.bsj-2019050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/12/2019] [Indexed: 12/01/2022] Open
Abstract
Protein functions can be predicted based on their three-dimensional structures. However, many multidomain proteins have unstable structures, making it difficult to determine the whole structure in biological experiments. Additionally, multidomain proteins are often decomposed and identified based on their domains, with the structure of each domain often found in public databases. Recent studies have advanced structure prediction methods of multidomain proteins through computational analysis. In existing methods, proteins that serve as templates are used for three-dimensional structure prediction. However, when no protein template is available, the accuracy of the prediction is decreased. This study was conducted to predict the structures of multidomain proteins without the need for whole structure templates. We improved structure prediction methods by performing rigid-body docking from the structure of each domain and reranking a structure closer to the correct structure to have a higher value. In the proposed method, the score for the domain-domain interaction obtained without a structural template of the multidomain protein and score for the three-dimensional structure obtained during docking calculation were newly incorporated into the score function. We successfully predicted the structures of 50 of 55 multidomain proteins examined in the test dataset. Interaction residue pair information of the protein-protein complex interface contributes to domain reorganizations even when a structural template for a multidomain protein cannot be obtained. This approach may be useful for predicting the structures of multidomain proteins with important biochemical functions.
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Affiliation(s)
- Shumpei Matsuno
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,AIST-TokyoTech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8560, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Kawasaki, Kanagawa 210-0821, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, Kawasaki, Kanagawa 210-0821, Japan
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31
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Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C. The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. BMC Evol Biol 2020; 20:30. [PMID: 32059645 PMCID: PMC7023805 DOI: 10.1186/s12862-020-1591-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/31/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Modularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. In proteins, this principle can be observed at the level of protein domains, functional subunits which are regularly rearranged to acquire new functions. RESULTS In this study we analyse the mechanisms leading to new domain arrangements in five major eukaryotic clades (vertebrates, insects, fungi, monocots and eudicots) at unprecedented depth and breadth. This allows, for the first time, to directly compare rates of rearrangements between different clades and identify both lineage specific and general patterns of evolution in the context of domain rearrangements. We analyse arrangement changes along phylogenetic trees by reconstructing ancestral domain content in combination with feasible single step events, such as fusion or fission. Using this approach we explain up to 70% of all rearrangements by tracing them back to their precursors. We find that rates in general and the ratio between these rates for a given clade in particular, are highly consistent across all clades. In agreement with previous studies, fusions are the most frequent event leading to new domain arrangements. A lineage specific pattern in fungi reveals exceptionally high loss rates compared to other clades, supporting recent studies highlighting the importance of loss for evolutionary innovation. Furthermore, our methodology allows us to link domain emergences at specific nodes in the phylogenetic tree to important functional developments, such as the origin of hair in mammals. CONCLUSIONS Our results demonstrate that domain rearrangements are based on a canonical set of mutational events with rates which lie within a relatively narrow and consistent range. In addition, gained knowledge about these rates provides a basis for advanced domain-based methodologies for phylogenetics and homology analysis which complement current sequence-based methods.
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Affiliation(s)
- Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany.,Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen, 45665, Germany
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany
| | - Sören Perrey
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen, 45665, Germany
| | - Carsten Kemena
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany.
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32
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Abstract
Background: Locating the root node of the "tree of life" (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA, and that Asgard archaea are sister to other archaea. The other 2D-ToL proposes that eukaryotes emerged from within archaea and places Asgard archaea as sister to eukaryotes. Williams et al. ( Nature Ecol. Evol. 4: 138-147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: The poor resolution of the archaea in their analysis, despite employing amino acid alignments from thousands of proteins and the best-fitting substitution models, contradicts their conclusions. We argue that they overlooked important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data. Which 2D-ToL is better supported depends on which kind of molecular features are better for resolving common ancestors at the roots of clades - protein-domains or their component amino acids. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. Clarifications: It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. We show that protein structural-domains support more reliable phylogenetic reconstructions of deep-diverging clades in the ToL. Accordingly, Eukaryotes and Akaryotes are better supported clades in a 2D-ToL.
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Affiliation(s)
| | - David Morrison
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, 752 36, Sweden
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33
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Singh V, Singh G, Singh V. TulsiPIN: An Interologous Protein Interactome of Ocimum tenuiflorum. J Proteome Res 2020; 19:884-899. [PMID: 31789043 DOI: 10.1021/acs.jproteome.9b00683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ocimum tenuiflorum, commonly known as holy basil or tulsi, is globally recognized for its multitude of medicinal properties. However, a comprehensive study revealing the complex interplay among its constituent proteins at subcellular level is still lacking. To bridge this gap, in this work, a genome-scale interologous protein-protein interaction (PPI) network, TulsiPIN, is developed using 36 template plants, which consists of 13 660 nodes and 327 409 binary interactions. A high confidence network, hc-TulsiPIN, consisting of 7719 nodes having 95 532 interactions is inferred using domain-domain interaction information along with interolog-based statistics, and its reliability is assessed using pathway enrichment, functional homogeneity, and protein colocalization of PPIs. Examination of topological features revealed that hc-TulsiPIN possesses conventional properties, like small-world, scale-free, and modular architecture. A total of 1625 vital proteins are predicted by statistically evaluating hc-TulsiPIN with two ensembles of corresponding random networks, each consisting of 10 000 realizations of Erdoős-Rényi and Barabási-Albert models. Also, numerous regulatory proteins like transcription factors, transcription regulators, and protein kinases are profiled. Using 36 guide genes participating in 9 secondary metabolite biosynthetic pathways, a subnetwork consisting of 171 proteins and 612 interactions was constructed, and 127 of these proteins could be successfully characterized. Detailed information of TulsiPIN is available at https://cuhpcbbtulsipin.shinyapps.io/tulsipin_v0/ .
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Affiliation(s)
- Vikram Singh
- Centre for Computational Biology and Bioinformatics , Central University of Himahcal Pradesh , Dharamshala 176206 , India
| | - Gagandeep Singh
- Centre for Computational Biology and Bioinformatics , Central University of Himahcal Pradesh , Dharamshala 176206 , India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics , Central University of Himahcal Pradesh , Dharamshala 176206 , India
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34
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Bigman LS, Levy Y. Proteins: molecules defined by their trade-offs. Curr Opin Struct Biol 2020; 60:50-56. [DOI: 10.1016/j.sbi.2019.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
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35
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Cotranslational Folding of Proteins on the Ribosome. Biomolecules 2020; 10:biom10010097. [PMID: 31936054 PMCID: PMC7023365 DOI: 10.3390/biom10010097] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/20/2019] [Accepted: 12/25/2019] [Indexed: 02/04/2023] Open
Abstract
Many proteins in the cell fold cotranslationally within the restricted space of the polypeptide exit tunnel or at the surface of the ribosome. A growing body of evidence suggests that the ribosome can alter the folding trajectory in many different ways. In this review, we summarize the recent examples of how translation affects folding of single-domain, multiple-domain and oligomeric proteins. The vectorial nature of translation, the spatial constraints of the exit tunnel, and the electrostatic properties of the ribosome-nascent peptide complex define the onset of early folding events. The ribosome can facilitate protein compaction, induce the formation of intermediates that are not observed in solution, or delay the onset of folding. Examples of single-domain proteins suggest that early compaction events can define the folding pathway for some types of domain structures. Folding of multi-domain proteins proceeds in a domain-wise fashion, with each domain having its role in stabilizing or destabilizing neighboring domains. Finally, the assembly of protein complexes can also begin cotranslationally. In all these cases, the ribosome helps the nascent protein to attain a native fold and avoid the kinetic traps of misfolding.
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36
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V K MA, Chandrasekaran VM, Pandurangan S. Protein Domain Level Cancer Drug Targets in the Network of MAPK Pathways. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:2057-2065. [PMID: 29993692 DOI: 10.1109/tcbb.2018.2829507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins in the MAPK pathways considered as potential drug targets for cancer treatment. Pathways along with the cross-talks increase their scope to view them as a network of MAPK pathways. Side effect causing targeted domains act as a proxy for drug targets due to its structural similarity and frequent reuse of their variants. We proposed to identify non-repeatable protein domains as the drug targets to disrupt the signal transduction than targeting the whole protein. Network based approach is used to understand the contribution of 52 domains in non-hub, non-essential, and intra-pathway cancerous nodes and to identify potential drug target domains. 34 distinct domains in the cancerous proteins are playing vital roles in making cancer as a complex disease and pose challenges to identify potential drug targets. Distribution of domain families follows the power law in the network. Single promiscuous domains are contributing to the formation of hubs like Pkinease, Pkinease Tyr, and Ras. Hub nodes are positively correlated with the domain coverage and targeting them would disrupt functional properties of the proteins. EIF 4EBP, alpha Kinase, Sel1, ROKNT, and KH 1 are the domains identified as potential domain targets for the disruption of the signaling mechanism involved in cancer.
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37
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Li Q, Scholl ZN, Marszalek PE. Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase. Biophys J 2019; 115:46-58. [PMID: 29972811 DOI: 10.1016/j.bpj.2018.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/31/2018] [Accepted: 05/21/2018] [Indexed: 01/12/2023] Open
Abstract
Phosphoglycerate kinase (PGK) is a highly conserved enzyme that is crucial for glycolysis. PGK is a monomeric protein composed of two similar domains and has been the focus of many studies for investigating interdomain interactions within the native state and during folding. Previous studies used traditional biophysical methods (such as circular dichroism, tryptophan fluorescence, and NMR) to measure signals over a large ensemble of molecules, which made it difficult to observe transient changes in stability or structure during unfolding and refolding of single molecules. Here, we unfold single molecules of PGK using atomic force spectroscopy and steered molecular dynamic computer simulations to examine the conformational dynamics of PGK during its unfolding process. Our results show that after the initial forced separation of its domains, yeast PGK (yPGK) does not follow a single mechanical unfolding pathway; instead, it stochastically follows two distinct pathways: unfolding from the N-terminal domain or unfolding from the C-terminal domain. The truncated yPGK N-terminal domain unfolds via a transient intermediate, whereas the structurally similar isolated C-terminal domain has no detectable intermediates throughout its mechanical unfolding process. The N-terminal domain in the full-length yPGK displays a strong unfolding intermediate 13% of the time, whereas the truncated domain (yPGKNT) transitions through the intermediate 81% of the time. This effect indicates that the mechanical properties of yPGK cannot be simply deduced from the mechanical properties of its constituents. We also find that Escherichia coli PGK is significantly less mechanically stable as compared to yPGK, contrary to bulk unfolding measurements. Our results support the growing body of observations that the folding behavior of multidomain proteins is difficult to predict based solely on the studies of isolated domains.
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Affiliation(s)
- Qing Li
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Piotr E Marszalek
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
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38
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Aizu T, Suzuki T, Kido A, Nagai K, Kobayashi A, Sugiura R, Ito Y, Mishima M. Domain selective labeling for NMR studies of multidomain proteins by domain ligation using highly active sortase A. Biochim Biophys Acta Gen Subj 2019; 1864:129419. [PMID: 31449838 DOI: 10.1016/j.bbagen.2019.129419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 11/19/2022]
Abstract
Structural study of multidomain proteins using NMR is an emerging issue for understanding biological functions. To this end, domain-specific labeling is expected to be a key technology for facilitating the NMR-assignment process and for collecting distance information via spin labeling. To obtain domain-specific labeled samples, use of sortase A as a protein ligation tool is a viable approach. Sortase A enables ligation of separately expressed proteins (domains) through the Leu-Pro-X-Thr-Gly linker. However, the ligation reaction mediated by sortase A is not efficient. Poor yield and long reaction times hamper large-scale preparation using sortase A. Here we report the application of highly active sortases to NMR analyses. Optimal yields can be achieved within several hours when the ligation reaction are mediated by highly active sortases at 4 °C. We propose that this protocol can contribute to structural analyses of multidomain proteins by NMR.
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Affiliation(s)
- Takahiro Aizu
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan
| | - Takumi Suzuki
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan
| | - Akihiro Kido
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan
| | - Kan Nagai
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan
| | - Ayaho Kobayashi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, 3-4-1 Kowake, Higashi-Osaka 577-8502, Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan
| | - Masaki Mishima
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji 192-0397, Japan.
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39
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Verma R, Pandit SB. Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions. PLoS One 2019; 14:e0220336. [PMID: 31374091 PMCID: PMC6677297 DOI: 10.1371/journal.pone.0220336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Intra-chain domain interactions are known to play a significant role in the function and stability of multidomain proteins. These interactions are mediated through a physical interaction at domain-domain interfaces (DDIs). With a motivation to understand evolution of interfaces, we have investigated similarities among DDIs. Even though interfaces of protein-protein interactions (PPIs) have been previously studied by structurally aligning interfaces, similar analyses have not yet been performed on DDIs of either multidomain proteins or PPIs. For studying the structural landscape of DDIs, we have used iAlign to structurally align intra-chain domain interfaces of domains. The interface alignment of spatially constrained domains (due to inter-domain linkers) showed that ~88% of these could identify a structural matching interface having similar C-alpha geometry and contact pattern despite that aligned domain pairs are not structurally related. Moreover, the mean interface similarity score (IS-score) is 0.307, which is higher compared to the average random IS-score (0.207) suggesting domain interfaces are not random. The structural space of DDIs is highly connected as ~84% of all possible directed edges among interfaces are found to have at most path length of 8 when 0.26 is IS-score threshold. At this threshold, ~83% of interfaces form the largest strongly connected component. Thus, suggesting that structural space of intra-chain domain interfaces is degenerate and highly connected, as has been found in PPI interfaces. Interestingly, searching for structural neighbors of inter-chain interfaces among intra-chain interfaces showed that ~86% could find a statistically significant match to intra-chain interface with a mean IS-score of 0.311. This implies that domain interfaces are degenerate whether formed within a protein or between proteins. The interface degeneracy is most likely due to limited possible ways of packing secondary structures. In principle, interface similarities can be exploited to accurately model domain interfaces in structure prediction of multidomain proteins.
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Affiliation(s)
- Rivi Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Shashi Bhushan Pandit
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
- * E-mail:
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40
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Basile W, Salvatore M, Bassot C, Elofsson A. Why do eukaryotic proteins contain more intrinsically disordered regions? PLoS Comput Biol 2019; 15:e1007186. [PMID: 31329574 PMCID: PMC6675126 DOI: 10.1371/journal.pcbi.1007186] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 08/01/2019] [Accepted: 06/14/2019] [Indexed: 12/12/2022] Open
Abstract
Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins. Methods predicting intrinsic disorder are based on the amino acid sequence of a protein. Therefore, there must exist an underlying difference in the sequences between eukaryotic and prokaryotic proteins causing the (predicted) difference in intrinsic disorder. By comparing proteins, from complete eukaryotic and prokaryotic proteomes, we show that the difference in intrinsic disorder emerges from the linker regions connecting Pfam domains. Eukaryotic proteins have more extended linker regions, and in addition, the eukaryotic linkers are significantly more disordered, 38% vs. 12-16% disordered residues. Next, we examined the underlying reason for the increase in disorder in eukaryotic linkers, and we found that the changes in abundance of only three amino acids cause the increase. Eukaryotic proteins contain 8.6% serine; while prokaryotic proteins have 6.5%, eukaryotic proteins also contain 5.4% proline and 5.3% isoleucine compared with 4.0% proline and ≈ 7.5% isoleucine in the prokaryotes. All these three differences contribute to the increased disorder in eukaryotic proteins. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. The differences are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. The observation that differences in the abundance of three amino acids cause the difference in disorder between eukaryotic and prokaryotic proteins raises the question: Are amino acid frequencies different in eukaryotic linkers because the linkers are more disordered or do the differences cause the increased disorder? Intrinsic disorder is essential for various functions in eukaryotic cells and is a signature of eukaryotic proteins. Here, we try to understand the origin of the difference in disorder between eukaryotic and prokaryotic proteins. We show that eukaryotic proteins contain more extended linker regions and that these linker regions are significantly more disordered. Further, we show, for the first time, that the difference in disorder originates from a systematic difference in amino acid frequencies between eukaryotic and prokaryotic proteins. Three amino acids contribute to the difference in disorder; serine and proline are more abundant in eukaryotic linkers, while isoleucine is less frequent. These shifts in frequencies are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. Anyhow the widespread of the shifts in abundance indicates that the differences are ancient and caused be some yet not fully understood selective difference acting on eukaryotic and prokaryotic proteins.
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Affiliation(s)
- Walter Basile
- Science for Life Laboratory, Stockholm University, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marco Salvatore
- Science for Life Laboratory, Stockholm University, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Claudio Bassot
- Science for Life Laboratory, Stockholm University, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Arne Elofsson
- Science for Life Laboratory, Stockholm University, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Swedish e-Science Research Center (SeRC), Stockholm, Sweden
- * E-mail:
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41
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Naveenkumar N, Kumar G, Sowdhamini R, Srinivasan N, Vishwanath S. Fold combinations in multi-domain proteins. Bioinformation 2019; 15:342-350. [PMID: 31249437 PMCID: PMC6589474 DOI: 10.6026/97320630015342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 01/21/2023] Open
Abstract
Domain-domain interactions in multi-domain proteins play an important role in the combined function of individual domains for the overall biological activity of the protein. The functions of the tethered domains are often coupled and hence, limited numbers of domain architectures with defined folds are known in nature. Therefore, it is of interest to document the available fold-fold combinations and their preference in multi-domain proteins. Hence, we analyzed all multi-domain proteins with known structures in the protein databank and observed that only about 860 fold-fold combinations are present among them. Analyses of multi-domain proteins represented in sequence database result in recognition of 29,860 fold-fold combinations and it accounts for only 2.8% of the theoretically possible 1,036,080 (1439C2) fold-fold combinations. The observed preference for fold-fold combinations in multi-domain proteins is interesting in the context of multiple functions through structural adaptation by gene fusion.
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Affiliation(s)
- Nagarajan Naveenkumar
- National Center for Biological Science, GKVK Campus, Bengaluru, Karnataka, India - 560065
- Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India - 560012
| | - Gayatri Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India - 560012
| | - Ramanathan Sowdhamini
- National Center for Biological Science, GKVK Campus, Bengaluru, Karnataka, India - 560065
| | | | - Sneha Vishwanath
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India - 560012
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42
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Abstract
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
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Affiliation(s)
| | - Sabeeha S Merchant
- Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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43
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Born A, Nichols PJ, Henen MA, Chi CN, Strotz D, Bayer P, Tate SI, Peng JW, Vögeli B. Backbone and side-chain chemical shift assignments of full-length, apo, human Pin1, a phosphoprotein regulator with interdomain allostery. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:85-89. [PMID: 30353504 PMCID: PMC9205186 DOI: 10.1007/s12104-018-9857-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/19/2018] [Indexed: 05/27/2023]
Abstract
Pin1 is a human peptidyl-prolyl cis-trans isomerase important for the regulation of phosphoproteins that are implicated in many diseases including cancer and Alzheimer's. Further biophysical study of Pin1 will elucidate the importance of the two-domain system to regulate its own activity. Here, we report near-complete backbone and side-chain 1H, 13C and 15N NMR chemical shift assignments of full-length, apo Pin1 for the purpose of studying interdomain allostery and dynamics.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123, Uppsala, Sweden
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zurich, Switzerland
| | - Peter Bayer
- Strukturelle und Medizinische Biochemie, Universität Duisburg-Essen, Universitätsstrasse 2-5, 45117, Essen, Germany
| | - Shin-Ichi Tate
- Department of Mathematical and Life Sciences, Hiroshima University, Hiroshima, Japan
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry & Department of Physics, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Research Center 1 South, Room 9103, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
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Debiec KT, Whitley MJ, Koharudin LMI, Chong LT, Gronenborn AM. Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein. Biophys J 2019; 114:839-855. [PMID: 29490245 DOI: 10.1016/j.bpj.2018.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/19/2017] [Accepted: 01/02/2018] [Indexed: 12/21/2022] Open
Abstract
Multidomain proteins with two or more independently folded functional domains are prevalent in nature. Whereas most multidomain proteins are linked linearly in sequence, roughly one-tenth possess domain insertions where a guest domain is implanted into a loop of a host domain, such that the two domains are connected by a pair of interdomain linkers. Here, we characterized the influence of the interdomain linkers on the structure and dynamics of a domain-insertion protein in which the guest LysM domain is inserted into a central loop of the host CVNH domain. Expanding upon our previous crystallographic and NMR studies, we applied SAXS in combination with NMR paramagnetic relaxation enhancement to construct a structural model of the overall two-domain system. Although the two domains have no fixed relative orientation, certain orientations were found to be preferred over others. We also assessed the accuracies of molecular mechanics force fields in modeling the structure and dynamics of tethered multidomain proteins by integrating our experimental results with microsecond-scale atomistic molecular dynamics simulations. In particular, our evaluation of two different combinations of the latest force fields and water models revealed that both combinations accurately reproduce certain structural and dynamical properties, but are inaccurate for others. Overall, our study illustrates the value of integrating experimental NMR and SAXS studies with long timescale atomistic simulations for characterizing structural ensembles of flexibly linked multidomain systems.
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Affiliation(s)
- Karl T Debiec
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Matthew J Whitley
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Leonardus M I Koharudin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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Abstract
Genomes appear similar to natural language texts, and protein domains can be treated as analogs of words. To investigate the linguistic properties of genomes further, we calculated the complexity of the “protein languages” in all major branches of life and identified a nearly universal value of information gain associated with the transition from a random domain arrangement to the current protein domain architecture. An exploration of the evolutionary relationship of the protein languages identified the domain combinations that discriminate between the major branches of cellular life. We conclude that there exists a “quasi-universal grammar” of protein domains and that the nearly constant information gain we identified corresponds to the minimal complexity required to maintain a functional cell. From an abstract, informational perspective, protein domains appear analogous to words in natural languages in which the rules of word association are dictated by linguistic rules, or grammar. Such rules exist for protein domains as well, because only a small fraction of all possible domain combinations is viable in evolution. We employ a popular linguistic technique, n-gram analysis, to probe the “proteome grammar”—that is, the rules of association of domains that generate various domain architectures of proteins. Comparison of the complexity measures of “protein languages” in major branches of life shows that the relative entropy difference (information gain) between the observed domain architectures and random domain combinations is highly conserved in evolution and is close to being a universal constant, at ∼1.2 bits. Substantial deviations from this constant are observed in only two major groups of organisms: a subset of Archaea that appears to be cells simplified to the limit, and animals that display extreme complexity. We also identify the n-grams that represent signatures of the major branches of cellular life. The results of this analysis bolster the analogy between genomes and natural language and show that a “quasi-universal grammar” underlies the evolution of domain architectures in all divisions of cellular life. The nearly universal value of information gain by the domain architectures could reflect the minimum complexity of signal processing that is required to maintain a functioning cell.
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Tambunan US, Parikesit AA, Ghifari AS, Satriyanto CP. In silico identification of 2-oxo-1,3-thiazolidine derivatives as novel inhibitor candidate of class II histone deacetylase (HDAC) in cervical cancer treatment. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2015.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Van Holle S, Van Damme EJM. Messages From the Past: New Insights in Plant Lectin Evolution. FRONTIERS IN PLANT SCIENCE 2019; 10:36. [PMID: 30761173 PMCID: PMC6362431 DOI: 10.3389/fpls.2019.00036] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/10/2019] [Indexed: 05/25/2023]
Abstract
Lectins are a large and diverse class of proteins, found in all kingdoms of life. Plants are known to express different types of carbohydrate-binding proteins, each containing at least one particular lectin domain which enables them to specifically recognize and bind carbohydrate structures. The group of plant lectins is heterogeneous in terms of structure, biological activity and function. Lectins control various aspects of plant development and defense. Some lectins facilitate recognition of exogenous danger signals or play a role in endogenous signaling pathways, while others are considered as storage proteins or involved in symbiotic relationships. In this study, we revisit the origin of the different plant lectin families in view of the recently reshaped tree of life. Due to new genomic sampling of previously unknown microbial lineages, the tree of life has expanded and was reshaped multiple times. In addition, more plant genomes especially from basal Phragmoplastophyta, bryophytes, and Salviniales (e.g., Chara braunii, Marchantia polymorpha, Physcomitrella patens, Azolla filiculoides, and Salvinia cucullata) have been analyzed, and annotated genome sequences have become accessible. We searched 38 plant genome sequences including core eudicots, monocots, gymnosperms, fern, lycophytes, bryophytes, charophytes, chlorophytes, glaucophytes, and rhodophytes for lectin motifs, performed an extensive comparative analysis of lectin domain architectures, and determined the phylogenetic and evolutionary history of lectins in the plant lineage. In conclusion, we describe the conservation of particular domains in plant lectin sequences obtained from algae to higher plants. The strong conservation of several lectin motifs highlights their significance for plants.
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A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria. Antonie van Leeuwenhoek 2018; 112:101-107. [PMID: 30171432 DOI: 10.1007/s10482-018-1154-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/28/2018] [Indexed: 01/18/2023]
Abstract
Protein functional domains are semi-autonomous parts of proteins capable of functioning independently. One protein may contain several domains and one domain may be present in different protein sequences. Thus, protein domains represent the niche specific adaptive nature of an organism. We hypothesized that the presence and absence of protein domains in an organism could be used to make a phylogenetic tree, which may better depict the biotope (niche). Here, we selected 100 actinobacteria and built a phylogenetic tree depending upon the presence and absence of protein domains. Strains of different genera from the same niche were found to cluster together suggesting niche specific domain acquisition among selected strains. Thus, the domain based phylogeny clustered the selected actinobacteria mainly according to their niche rather than their taxonomic classification.
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Makabe K, Nakamura T, Dhar D, Ikura T, Koide S, Kuwajima K. An Overlapping Region between the Two Terminal Folding Units of the Outer Surface Protein A (OspA) Controls Its Folding Behavior. J Mol Biol 2018; 430:1799-1813. [PMID: 29709572 DOI: 10.1016/j.jmb.2018.04.025] [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: 12/14/2017] [Revised: 04/12/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
Abstract
Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions.
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Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata 992-8510, Japan; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
| | - Takashi Nakamura
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Debanjan Dhar
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Teikichi Ikura
- Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, and Perlmutter Cancer Center at NYU Langone Health, New York, NY 10016, USA
| | - Kunihiro Kuwajima
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Dongdaemun-gu, Seoul 130-722, Korea
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