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Aduriz-Arrizabalaga J, Lopez X, De Sancho D. Atomistic molecular simulations of Aβ-Zn conformational ensembles. Proteins 2024; 92:134-144. [PMID: 37746887 DOI: 10.1002/prot.26590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
The amyloid-forming Aβ peptide is able to interact with metal cations to form very stable complexes that influence fibril formation and contribute to the onset of Alzheimer's disease. Multiple structures of peptides derived from Aβ in complex with different metals have been resolved experimentally to provide an atomic-level description of the metal-protein interactions. However, Aβ is intrinsically disordered, and hence more amenable to an ensemble description. Molecular dynamics simulations can now reach the timescales needed to generate ensembles for these type of complexes. However, this requires accurate force fields both for the protein and the protein-metal interactions. Here we use state-of-the-art methods to generate force field parameters for the Zn(II) cations in a set of complexes formed by different Aβ variants and combine them with the Amber99SB*-ILDN optimized force field. Upon comparison of NMR experiments with the simulation results, further optimized with a Bayesian/Maximum entropy approach, we provide an accurate description of the molecular ensembles for most Aβ-metal complexes. We find that the resulting conformational ensembles are more heterogeneous than the NMR models deposited in the Protein Data Bank.
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Affiliation(s)
- Julen Aduriz-Arrizabalaga
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
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Pichon NA, Cappelli SL, Soliveres S, Mannall T, Nwe TZ, Hölzel N, Klaus VH, Kleinebecker T, Vincent H, Allan E. Nitrogen availability and plant functional composition modify biodiversity-multifunctionality relationships. Ecol Lett 2024; 27:e14361. [PMID: 38217282 DOI: 10.1111/ele.14361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/15/2024]
Abstract
Biodiversity typically increases multiple ecosystem functions simultaneously (multifunctionality) but variation in the strength and direction of biodiversity effects between studies suggests context dependency. To determine how different factors modulate the diversity effect on multifunctionality, we established a large grassland experiment manipulating plant species richness, resource addition, functional composition (exploitative vs. conservative species), functional diversity and enemy abundance. We measured ten above- and belowground functions and calculated ecosystem multifunctionality. Species richness and functional diversity both increased multifunctionality, but their effects were context dependent. Richness increased multifunctionality when communities were assembled with fast-growing species. This was because slow species were more redundant in their functional effects, whereas different fast species promoted different functions. Functional diversity also increased multifunctionality but this effect was dampened by nitrogen enrichment and enemy presence. Our study suggests that a shift towards fast-growing communities will not only alter ecosystem functioning but also the strength of biodiversity-functioning relationships.
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Affiliation(s)
- Noémie A Pichon
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Seraina L Cappelli
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Santiago Soliveres
- Department of Ecology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
| | - Tosca Mannall
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Thu Zar Nwe
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Valentin H Klaus
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, Zürich, Switzerland
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
| | - Till Kleinebecker
- Department of Landscape Ecology and Resources Management, Justus-Liebig-University Gießen, Giessen, Germany
| | - Hugo Vincent
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Eric Allan
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Centre for Development and the Environment, University of Bern, Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
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de la Riva EG, Prieto I, de Tomás Marín S, Rodríguez-Calcerrada J, Golabvand P, Galán Díaz J. Living at the edge: the functional niche occupation of woody plant communities in the submediterranean ecotone. Ann Bot 2023; 132:471-484. [PMID: 37724864 PMCID: PMC10666996 DOI: 10.1093/aob/mcad138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND AND AIMS Submediterranean areas are rich ecotones, where slight modifications in environmental conditions can lead to substantial changes in the composition of plant communities. They thus offer an ideal scenario to examine plant community assembly. In this study, we followed a trait-based approach including intraspecific variability to elucidate (1) the relationship between niche occupancy components and species richness, (2) the processes governing the assembly of these communities and (3) the contribution of intraspecific trait variability in shaping the functional trait space. METHODS We measured eight morphological and chemical traits in 405 individuals across 60 plots located in different forest communities (Mediterranean, Eurosiberian and Mixed) coexisting within a submediterranean ecosystem in central Spain. We calculated three niche occupancy components related to Hutchinson's n-dimensional hypervolumes: the total functional volume of the community, the functional overlap between species within the community and the average functional volume per species, and then used null models to explore the relative importance of habitat filtering, limiting similarity and intraspecific variability as assembly patterns. KEY RESULTS Both habitat filtering and niche differentiation drive the community assembly of Mediterranean communities, whereas limiting similarity and hierarchical competition shape Eurosiberian communities. Intraspecific responses were mostly explained by shifts in species niches across the functional space (changes in the position of the centroids of hypervolumes). CONCLUSIONS Different assembly mechanisms govern the structure of Mediterranean, Eurosiberian and Mixed plant communities. Combining niche occupancy components with a null model approach at different spatial scales offers new insights into the mechanisms driving plant community assembly. Consideration of intraspecific variability is key for understanding the mechanisms governing species coexistence in species-rich ecotones.
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Affiliation(s)
- Enrique G de la Riva
- Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
- Department of Ecology, Brandenburg University of Technology, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Iván Prieto
- Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Sergio de Tomás Marín
- Department of Ecology, Brandenburg University of Technology, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Jesús Rodríguez-Calcerrada
- Functioning of Forest Systems in a Changing Environment (FORESCENT), Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Pardis Golabvand
- Department of Ecology, Brandenburg University of Technology, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Javier Galán Díaz
- Department of Plant Biology and Ecology, Universidad of Sevilla, 41012 Sevilla, Spain
- Department of Pharmacology, Pharmacognosy and Botany, Universidad Complutense de Madrid, 28040 Madrid, Spain
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González-Delgado S, Wangensteen OS, Sangil C, Hernández CA, Alfonso B, Soto AZ, Pérez-Portela R, Mariani S, Hernández JC. High taxonomic diversity and miniaturization in benthic communities under persistent natural CO 2 disturbances. Proc Biol Sci 2023; 290:20222417. [PMID: 36987638 PMCID: PMC10050917 DOI: 10.1098/rspb.2022.2417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Metabarcoding techniques have revolutionized ecological research in recent years, facilitating the differentiation of cryptic species and revealing previously hidden diversity. In the current scenario of climate change and ocean acidification, biodiversity loss is one of the main threats to marine ecosystems. Here, we explored the effects of ocean acidification on marine benthic communities using DNA metabarcoding to assess the diversity of algae and metazoans. Specifically, we examined the natural pH gradient generated by the Fuencaliente CO2 vent system, located near La Palma Island (Canary Islands). High-resolution COI metabarcoding analyses revealed high levels of taxonomic diversity in an acidified natural area for the first time. This high number of species arises from the detection of small and cryptic species that were previously undetectable by other techniques. Such species are apparently tolerant to the acidification levels expected in future oceans. Hence and following our results, future subtropical communities are expected to keep high biodiversity values under an acidification scenario, although they will tend toward overall miniaturization due to the dominance of small algal and invertebrate species, leading to changes in ecosystem functions.
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Affiliation(s)
- Sara González-Delgado
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Canary Islands, Spain
| | - Owen S. Wangensteen
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Spain
| | - Carlos Sangil
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Canary Islands, Spain
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Canary Islands, Spain
| | - Celso A. Hernández
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Canary Islands, Spain
| | - Beatriz Alfonso
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Canary Islands, Spain
| | - Ana Z. Soto
- Apis Assay Technologies Ltd, Manchester M13 9NQ, UK
| | - Rocío Pérez-Portela
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Spain
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - José Carlos Hernández
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Canary Islands, Spain
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