1
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Park H, Patel P, Haas R, Huerta EA. APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. Proc Natl Acad Sci U S A 2024; 121:e2311888121. [PMID: 38913887 PMCID: PMC11228474 DOI: 10.1073/pnas.2311888121] [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: 08/14/2023] [Accepted: 12/25/2023] [Indexed: 06/26/2024] Open
Abstract
The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.
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Affiliation(s)
- Hyun Park
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parth Patel
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Roland Haas
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - E A Huerta
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Department of Computer Science, The University of Chicago, Chicago, IL 60637
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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2
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Bui HB, Inaba K. Structures, Mechanisms, and Physiological Functions of Zinc Transporters in Different Biological Kingdoms. Int J Mol Sci 2024; 25:3045. [PMID: 38474291 DOI: 10.3390/ijms25053045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024] Open
Abstract
Zinc transporters take up/release zinc ions (Zn2+) across biological membranes and maintain intracellular and intra-organellar Zn2+ homeostasis. Since this process requires a series of conformational changes in the transporters, detailed information about the structures of different reaction intermediates is required for a comprehensive understanding of their Zn2+ transport mechanisms. Recently, various Zn2+ transport systems have been identified in bacteria, yeasts, plants, and humans. Based on structural analyses of human ZnT7, human ZnT8, and bacterial YiiP, we propose updated models explaining their mechanisms of action to ensure efficient Zn2+ transport. We place particular focus on the mechanistic roles of the histidine-rich loop shared by several zinc transporters, which facilitates Zn2+ recruitment to the transmembrane Zn2+-binding site. This review provides an extensive overview of the structures, mechanisms, and physiological functions of zinc transporters in different biological kingdoms.
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Affiliation(s)
- Han Ba Bui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo 100-0004, Japan
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3
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Nussinov R, Liu Y, Zhang W, Jang H. Cell phenotypes can be predicted from propensities of protein conformations. Curr Opin Struct Biol 2023; 83:102722. [PMID: 37871498 PMCID: PMC10841533 DOI: 10.1016/j.sbi.2023.102722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of the conformations can be predictors of cell function. The conformational states that the molecules preferentially visit can be viewed as phenotypic determinants, and their mutations work by altering the relative propensities, thus the cell phenotype. Our examples include (i) inactive state variants harboring cancer driver mutations that present active state-like conformational features, as in K-Ras4BG12V compared to other K-Ras4BG12X mutations; (ii) mutants of the same protein presenting vastly different phenotypic and clinical profiles: cancer and neurodevelopmental disorders; (iii) alterations in the occupancies of the conformational (sub)states influencing enzyme reactivity. Thus, protein conformational propensities can determine cell fate. They can also suggest the allosteric drugs efficiency.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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4
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Hussein A, Fan S, Lopez-Redondo M, Kenney I, Zhang X, Beckstein O, Stokes DL. Energy coupling and stoichiometry of Zn 2+/H + antiport by the prokaryotic cation diffusion facilitator YiiP. eLife 2023; 12:RP87167. [PMID: 37906094 PMCID: PMC10617992 DOI: 10.7554/elife.87167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
YiiP from Shewanella oneidensis is a prokaryotic Zn2+/H+ antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn2+ to 2-3 H+ depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn2+.
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Affiliation(s)
- Adel Hussein
- Department of Biochemistry and Molecular Pharmacology, NYU School of MedicineNew YorkUnited States
| | - Shujie Fan
- Department of Physics, Arizona State UniversityTempeUnited States
| | - Maria Lopez-Redondo
- Department of Biochemistry and Molecular Pharmacology, NYU School of MedicineNew YorkUnited States
| | - Ian Kenney
- Department of Physics, Arizona State UniversityTempeUnited States
| | - Xihui Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU School of MedicineNew YorkUnited States
| | - Oliver Beckstein
- Department of Physics, Arizona State UniversityTempeUnited States
| | - David L Stokes
- Department of Biochemistry and Molecular Pharmacology, NYU School of MedicineNew YorkUnited States
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5
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Sala D, Engelberger F, Mchaourab HS, Meiler J. Modeling conformational states of proteins with AlphaFold. Curr Opin Struct Biol 2023; 81:102645. [PMID: 37392556 DOI: 10.1016/j.sbi.2023.102645] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 07/03/2023]
Abstract
Many proteins exert their function by switching among different structures. Knowing the conformational ensembles affiliated with these states is critical to elucidate key mechanistic aspects that govern protein function. While experimental determination efforts are still bottlenecked by cost, time, and technical challenges, the machine-learning technology AlphaFold showed near experimental accuracy in predicting the three-dimensional structure of monomeric proteins. However, an AlphaFold ensemble of models usually represents a single conformational state with minimal structural heterogeneity. Consequently, several pipelines have been proposed to either expand the structural breadth of an ensemble or bias the prediction toward a desired conformational state. Here, we analyze how those pipelines work, what they can and cannot predict, and future directions.
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Affiliation(s)
- D Sala
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany. https://twitter.com/sala_davide
| | - F Engelberger
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany. https://twitter.com/fengel97
| | - H S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA. https://twitter.com/Mchaourablab
| | - J Meiler
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig, Germany.
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6
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Hussein A, Fan S, Lopez-Redondo M, Kenney I, Zhang X, Beckstein O, Stokes DL. Energy Coupling and Stoichiometry of Zn 2+/H + Antiport by the Cation Diffusion Facilitator YiiP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529644. [PMID: 36865113 PMCID: PMC9980050 DOI: 10.1101/2023.02.23.529644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
YiiP is a prokaryotic Zn2+/H+ antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn2+ to 2-3 H+ depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn2+.
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Affiliation(s)
- Adel Hussein
- Dept. of Cell Biology, NYU School of Medicine, New York, NY 10016 USA
| | - Shujie Fan
- Dept. of Physics, Arizona State University, Tempe AZ
| | | | - Ian Kenney
- Dept. of Physics, Arizona State University, Tempe AZ
| | - Xihui Zhang
- Dept. of Cell Biology, NYU School of Medicine, New York, NY 10016 USA
| | | | - David L Stokes
- Dept. of Cell Biology, NYU School of Medicine, New York, NY 10016 USA
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7
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Yin S, Duan M, Fang B, Zhao G, Leng X, Zhang T. Zinc homeostasis and regulation: Zinc transmembrane transport through transporters. Crit Rev Food Sci Nutr 2022; 63:7627-7637. [PMID: 35258351 DOI: 10.1080/10408398.2022.2048292] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The second abundant micronutrient, zinc, is attracting more and more attention for it performs essential functions in living organisms and bears close relationships with the occurrence of diseases. However, excess zinc is toxic to cells. Ensuring a balanced zinc state for organisms is essential. Zinc transporters, including ZIPs and ZnTs, are pivotal in regulating zinc homeostasis. Benefiting from zinc transporter structures determination and their transporting dynamic revelation, the clarification of detailed mechanisms of zinc trafficking and the maintenance of zinc homeostasis by transporters in the human body are getting more and more evident. The present review gives a detailed description of the structural basis of zinc transport through ZIP and ZnT, through which the molecular mechanism of zinc binding and transport was illustrated. Then the motive force that drives zinc transmembrane transport and finally a generalization for the regulation models of zinc transporters were summarized.
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Affiliation(s)
- Shuhua Yin
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Maoping Duan
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Bing Fang
- Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Guanghua Zhao
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xiaojing Leng
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Tuo Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Nutrition and Health, China Agricultural University, Beijing, China
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8
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Sharma G, Merz KM. Mechanism of Zinc Transport through the Zinc Transporter YiiP. J Chem Theory Comput 2022; 18:2556-2568. [PMID: 35226479 DOI: 10.1021/acs.jctc.1c00927] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zinc is an essential transition metal ion that plays as a structural, functional (catalytic), and a signaling molecule regulating cellular function. Unbalanced levels of zinc in cells can result in various pathological conditions. In the current work, all-atom molecular dynamics simulations were used to study the structure-function correlation between different YiiP states embedded in a lipid bilayer. This study enabled us to develop a hypothesis on the zinc efflux mechanism of YiiP. We have created six different models of YiiP representing the stages of the ion-transport process. We found that zinc ion plays a crucial role in restraining the transmembrane domains (TMDs) of the protein. In addition, H153, located in the TMD, has been proposed to guide the zinc ion toward the ZnA site of the YiiP transporter. Understanding the molecular-level Zn2+-transport process sheds light on the strategies affecting intracellular transition-metal ion concentrations in order to treat diseases like diabetes and cancer.
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Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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9
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Lopez-Redondo M, Fan S, Koide A, Koide S, Beckstein O, Stokes DL. Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. J Gen Physiol 2021; 153:212464. [PMID: 34254979 PMCID: PMC8282283 DOI: 10.1085/jgp.202112873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle.
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Affiliation(s)
- Maria Lopez-Redondo
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY
| | - Shujie Fan
- Department of Physics, Arizona State University, Tempe, AZ
| | - Akiko Koide
- Perlmutter Cancer Center, Department of Medicine, New York University School of Medicine, New York, NY
| | - Shohei Koide
- Perlmutter Cancer Center, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY
| | | | - David L Stokes
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY
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10
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Barber-Zucker S, Moran A, Zarivach R. Metal transport mechanism of the cation diffusion facilitator (CDF) protein family - a structural perspective on human CDF (ZnT)-related diseases. RSC Chem Biol 2021; 2:486-498. [PMID: 34458794 PMCID: PMC8341793 DOI: 10.1039/d0cb00181c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/26/2020] [Indexed: 11/21/2022] Open
Abstract
Divalent d-block metal cations (DDMCs) participate in many cellular functions; however, their accumulation in cells can be cytotoxic. The cation diffusion facilitator (CDF) family is a ubiquitous family of transmembrane DDMC exporters that ensures their homeostasis. Severe diseases, such as type II diabetes, Parkinson's and Alzheimer's disease, were linked to dysfunctional human CDF proteins, ZnT-1-10 (SLC30A1-10). Each member of the CDF family reduces the cytosolic concentration of a specific DDMC by transporting it from the cytoplasm to the extracellular environment or into intracellular compartments. This process is usually achieved by utilizing the proton motive force. In addition to their activity as DDMC transporters, CDFs also have other cellular functions such as the regulation of ion channels and enzymatic activity. The combination of structural and biophysical studies of different bacterial and eukaryotic CDF proteins led to significant progress in the understanding of the mutual interaction among CDFs and DDMCs, their involvement in ion binding and selectivity, conformational changes and the consequent transporting mechanisms. Here, we review these studies, provide our mechanistic interpretation of CDF proteins based on the current literature and relate the above to known human CDF-related diseases. Our analysis provides a common structure-function relationship to this important protein family and closes the gap between eukaryote and prokaryote CDFs.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Life Sciences, the National Institute for Biotechnology in the Negev and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev P.O.B. 653 Beer Sheva 8410501 Israel +972-8-6472970 +972-8-6472970 +972-8-6428447 +972-8-6461999
| | - Arie Moran
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev P.O.B. 653 Beer Sheva 8410501 Israel
| | - Raz Zarivach
- Department of Life Sciences, the National Institute for Biotechnology in the Negev and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev P.O.B. 653 Beer Sheva 8410501 Israel +972-8-6472970 +972-8-6472970 +972-8-6428447 +972-8-6461999
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11
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Russum S, Lam KJK, Wong NA, Iddamsetty V, Hendargo KJ, Wang J, Dubey A, Zhang Y, Medrano-Soto A, Saier MH. Comparative population genomic analyses of transporters within the Asgard archaeal superphylum. PLoS One 2021; 16:e0247806. [PMID: 33770091 PMCID: PMC7997004 DOI: 10.1371/journal.pone.0247806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.
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Affiliation(s)
- Steven Russum
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Katie Jing Kay Lam
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Nicholas Alan Wong
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Vasu Iddamsetty
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Kevin J. Hendargo
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Jianing Wang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Aditi Dubey
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Yichi Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Arturo Medrano-Soto
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
| | - Milton H. Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
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12
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Sala D, Giachetti A, Rosato A. Insights into the Dynamics of the Human Zinc Transporter ZnT8 by MD Simulations. J Chem Inf Model 2021; 61:901-912. [PMID: 33508935 PMCID: PMC8023586 DOI: 10.1021/acs.jcim.0c01139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 02/07/2023]
Abstract
ZnT8 is a human zinc(II) transporter expressed at the membrane of secretory granules where it contributes to insulin storage importing zinc ions from the cytosol. In the human population, the two most common ZnT8 variants carry an arginine (R325) or a tryptophan (W325) in position 325. The former variant has the most efficient kinetics in zinc transport and has been correlated to a higher risk of developing insulin resistance. On the contrary, the W325 variant is less active and protects against type-2-diabetes. Here, we used molecular dynamics (MD) simulations to investigate the main differences between the R325 and W325 variants in the interaction with zinc(II) ions. Our simulations suggested that the position of the metal ion within the transport site was not the same for the two variants, underlying a different rearrangement of the transmembrane (TM) helices in the channel. The W325 variant featured a peculiar zinc environment not detected in the experimental structures. With respect to conformational dynamics, we observed that the R325 variant was significantly more flexible than W325, with the main role played by the transmembrane domain (TMD) and the C-terminal domain (CTD). This dynamics affected the packing of the TM helices and thus the channel accessibility from the cytosol. The dimer interface that keeps the two TM channels in contact became looser in both variants upon zinc binding to the transport site, suggesting that this may be an important step toward the switch from the inward- to the outward-facing state of the protein.
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Affiliation(s)
- Davide Sala
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Andrea Giachetti
- Consorzio
Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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