1
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Andrikopoulos PC, Čabart P. The chromatin remodeler SMARCA5 binds to d-block metal supports: Characterization of affinities by IMAC chromatography and QM analysis. PLoS One 2024; 19:e0309134. [PMID: 39374200 PMCID: PMC11458017 DOI: 10.1371/journal.pone.0309134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/05/2024] [Indexed: 10/09/2024] Open
Abstract
The ISWI family protein SMARCA5 contains the ATP-binding pocket that coordinates the catalytic Mg2+ ion and water molecules for ATP hydrolysis. In this study, we demonstrate that SMARCA5 can also possess an alternative metal-binding ability. First, we isolated SMARCA5 on the cobalt column (IMAC) to near homogeneity. Examination of the interactions of SMARCA5 with metal-chelating supports showed that, apart from Co2+, it binds to Cu2+, Zn2+ and Ni2+. The efficiency of the binding to the last-listed metal was influenced by the chelating ligand, resulting in a strong preference for Ni-NTA over the Ni-CM-Asp equivalent. To gain insight in the preferential affinity for the Ni-NTA ligand, QM calculations were performed on model systems and metal-ligand complexes with a limited protein fragment of SMARCA5 containing the double-histidine (dHis) motif. The calculations correlated the observed affinity with the relative stability of the d-block metals to tetradentate ligand coordination over tridentate, as well as their overall octahedral coordination capacity. Likewise, binding free energies derived from model imidazole complexes mirrored the observed Ni-NTA/Ni-CM-Asp preferential affinity. Finally, similar calculations on complexes with a SMARCA5 peptide fragment derived from the AlphaFold structural prediction, captured almost accurately the expected relative stability of the TM complexes, and produced a large energetic separation (~10 kcal∙mol-1) between Ni-NTA and Ni-CM-Asp in favour of the former.
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Affiliation(s)
- Prokopis C. Andrikopoulos
- BIOCEV, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- BIOCEV, 1 Faculty of Medicine, Charles University, Vestec, Czechia
| | - Pavel Čabart
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
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2
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Ding ZJ, Xu C, Yan JY, Wang YX, Cui MQ, Yuan JJ, Wang YN, Li GX, Wu JX, Wu YR, Xu JM, Li CX, Shi YZ, Mao CZ, Guo JT, Zhou JM, Benhamed M, Harberd NP, Zheng SJ. The LRR receptor-like kinase ALR1 is a plant aluminum ion sensor. Cell Res 2024; 34:281-294. [PMID: 38200278 PMCID: PMC10978910 DOI: 10.1038/s41422-023-00915-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Plant survival requires an ability to adapt to differing concentrations of nutrient and toxic soil ions, yet ion sensors and associated signaling pathways are mostly unknown. Aluminum (Al) ions are highly phytotoxic, and cause severe crop yield loss and forest decline on acidic soils which represent ∼30% of land areas worldwide. Here we found an Arabidopsis mutant hypersensitive to Al. The gene encoding a leucine-rich-repeat receptor-like kinase, was named Al Resistance1 (ALR1). Al ions binding to ALR1 cytoplasmic domain recruits BAK1 co-receptor kinase and promotes ALR1-dependent phosphorylation of the NADPH oxidase RbohD, thereby enhancing reactive oxygen species (ROS) generation. ROS in turn oxidatively modify the RAE1 F-box protein to inhibit RAE1-dependent proteolysis of the central regulator STOP1, thus activating organic acid anion secretion to detoxify Al. These findings establish ALR1 as an Al ion receptor that confers resistance through an integrated Al-triggered signaling pathway, providing novel insights into ion-sensing mechanisms in living organisms, and enabling future molecular breeding of acid-soil-tolerant crops and trees, with huge potential for enhancing both global food security and forest restoration.
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Affiliation(s)
- Zhong Jie Ding
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chen Xu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jing Ying Yan
- Agricultural Experimental Station, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Xuan Wang
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Meng Qi Cui
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Jie Yuan
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ya Nan Wang
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Gui Xin Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian Xiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yun Rong Wu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ji Ming Xu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun Xiao Li
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan Zhi Shi
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Chuan Zao Mao
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiang Tao Guo
- Medical School, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian Min Zhou
- Center for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Nicholas P Harberd
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Biology, University of Oxford, Oxford, UK
| | - Shao Jian Zheng
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China.
- Institute of Ecological Civilization, Zhejiang University, Hangzhou, Zhejiang, China.
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3
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Warnhoff K, Bhattacharya S, Snoozy J, Breen PC, Ruvkun G. Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans. eLife 2024; 12:RP89173. [PMID: 38349720 PMCID: PMC10942545 DOI: 10.7554/elife.89173] [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] [Indexed: 02/15/2024] Open
Abstract
Dedicated genetic pathways regulate cysteine homeostasis. For example, high levels of cysteine activate cysteine dioxygenase, a key enzyme in cysteine catabolism in most animal and many fungal species. The mechanism by which cysteine dioxygenase is regulated is largely unknown. In an unbiased genetic screen for mutations that activate cysteine dioxygenase (cdo-1) in the nematode Caenorhabditis elegans, we isolated loss-of-function mutations in rhy-1 and egl-9, which encode proteins that negatively regulate the stability or activity of the oxygen-sensing hypoxia inducible transcription factor (hif-1). EGL-9 and HIF-1 are core members of the conserved eukaryotic hypoxia response. However, we demonstrate that the mechanism of HIF-1-mediated induction of cdo-1 is largely independent of EGL-9 prolyl hydroxylase activity and the von Hippel-Lindau E3 ubiquitin ligase, the classical hypoxia signaling pathway components. We demonstrate that C. elegans cdo-1 is transcriptionally activated by high levels of cysteine and hif-1. hif-1-dependent activation of cdo-1 occurs downstream of an H2S-sensing pathway that includes rhy-1, cysl-1, and egl-9. cdo-1 transcription is primarily activated in the hypodermis where it is also sufficient to drive sulfur amino acid metabolism. Thus, the regulation of cdo-1 by hif-1 reveals a negative feedback loop that maintains cysteine homeostasis. High levels of cysteine stimulate the production of an H2S signal. H2S then acts through the rhy-1/cysl-1/egl-9 signaling pathway to increase HIF-1-mediated transcription of cdo-1, promoting degradation of cysteine via CDO-1.
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Affiliation(s)
- Kurt Warnhoff
- Pediatrics and Rare Diseases Group, Sanford ResearchSioux FallsUnited States
- Department of Pediatrics, Sanford School of Medicine, University of South DakotaSioux FallsUnited States
| | | | - Jennifer Snoozy
- Pediatrics and Rare Diseases Group, Sanford ResearchSioux FallsUnited States
| | - Peter C Breen
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
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4
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Ding Y, Huang J. DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. J Phys Chem Lett 2024; 15:616-627. [PMID: 38198685 DOI: 10.1021/acs.jpclett.3c03158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling.
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Affiliation(s)
- Ye Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
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5
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Shenoy A, Kalakoti Y, Sundar D, Elofsson A. M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings. Bioinformatics 2024; 40:btad782. [PMID: 38175787 PMCID: PMC10792727 DOI: 10.1093/bioinformatics/btad782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
MOTIVATION Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal-binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (pLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments). Using residue-level embeddings from the pLMs, we have developed a sequence-based method (M-Ionic) to identify metal-binding proteins and predict residues involved in metal binding. RESULTS On independent validation of recent proteins, M-Ionic reports an area under the curve (AUROC) of 0.83 (recall = 84.6%) in distinguishing metal binding from non-binding proteins compared to AUROC of 0.74 (recall = 61.8%) of the next best method. In addition to comparable performance to the state-of-the-art method for identifying metal-binding residues (Ca2+, Mg2+, Mn2+, Zn2+), M-Ionic provides binding probabilities for six additional ions (i.e. Cu2+, Po43-, So42-, Fe2+, Fe3+, Co2+). We show that the pLM embedding of a single residue contains sufficient information about its neighbours to predict its binding properties. AVAILABILITY AND IMPLEMENTATION M-Ionic can be used on your protein of interest using a Google Colab Notebook (https://bit.ly/40FrRbK). The GitHub repository (https://github.com/TeamSundar/m-ionic) contains all code and data.
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Affiliation(s)
- Aditi Shenoy
- Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Solna 17121, Sweden
| | - Yogesh Kalakoti
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
| | - Durai Sundar
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
- Yardi School of Artificial Intelligence, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
| | - Arne Elofsson
- Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Solna 17121, Sweden
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6
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Warnhoff K, Bhattacharya S, Snoozy J, Breen PC, Ruvkun G. Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.538701. [PMID: 37205365 PMCID: PMC10187278 DOI: 10.1101/2023.05.04.538701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Dedicated genetic pathways regulate cysteine homeostasis. For example, high levels of cysteine activate cysteine dioxygenase, a key enzyme in cysteine catabolism in most animal and many fungal species. The mechanism by which cysteine dioxygenase is regulated is largely unknown. In an unbiased genetic screen for mutations that activate cysteine dioxygenase (cdo-1) in the nematode C. elegans, we isolated loss-of-function mutations in rhy-1 and egl-9, which encode proteins that negatively regulate the stability or activity of the oxygen-sensing hypoxia inducible transcription factor (hif-1). EGL-9 and HIF-1 are core members of the conserved eukaryotic hypoxia response. However, we demonstrate that the mechanism of HIF-1-mediated induction of cdo-1 is largely independent of EGL-9 prolyl hydroxylase activity and the von Hippel-Lindau E3 ubiquitin ligase, the classical hypoxia signaling pathway components. We demonstrate that C. elegans cdo-1 is transcriptionally activated by high levels of cysteine and hif-1. hif-1-dependent activation of cdo-1 occurs downstream of an H2S-sensing pathway that includes rhy-1, cysl-1, and egl-9. cdo-1 transcription is primarily activated in the hypodermis where it is also sufficient to drive sulfur amino acid metabolism. Thus, the regulation of cdo-1 by hif-1 reveals a negative feedback loop that maintains cysteine homeostasis. High levels of cysteine stimulate the production of an H2S signal. H2S then acts through the rhy-1/cysl-1/egl-9 signaling pathway to increase HIF-1-mediated transcription of cdo-1, promoting degradation of cysteine via CDO-1.
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Affiliation(s)
- Kurt Warnhoff
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105 USA
| | - Sushila Bhattacharya
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Jennifer Snoozy
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Peter C. Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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7
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Essien C, Jiang L, Wang D, Xu D. Prediction of Protein Ion-Ligand Binding Sites with ELECTRA. Molecules 2023; 28:6793. [PMID: 37836636 PMCID: PMC10574437 DOI: 10.3390/molecules28196793] [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: 08/25/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Interactions between proteins and ions are essential for various biological functions like structural stability, metabolism, and signal transport. Given that more than half of all proteins bind to ions, it is becoming crucial to identify ion-binding sites. The accurate identification of protein-ion binding sites helps us to understand proteins' biological functions and plays a significant role in drug discovery. While several computational approaches have been proposed, this remains a challenging problem due to the small size and high versatility of metals and acid radicals. In this study, we propose IonPred, a sequence-based approach that employs ELECTRA (Efficiently Learning an Encoder that Classifies Token Replacements Accurately) to predict ion-binding sites using only raw protein sequences. We successfully fine-tuned our pretrained model to predict the binding sites for nine metal ions (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, and K+) and four acid radical ion ligands (CO32-, SO42-, PO43-, NO2-). IonPred surpassed six current state-of-the-art tools by over 44.65% and 28.46%, respectively, in the F1 score and MCC when compared on an independent test dataset. Our method is more computationally efficient than existing tools, producing prediction results for a hundred sequences for a specific ion in under ten minutes.
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Affiliation(s)
| | | | | | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (C.E.); (L.J.); (D.W.)
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8
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Song J, Khare E, Rao L, Buehler MJ, Holten-Andersen N. Coordination Stoichiometry Effects on the Binding Hierarchy of Histamine and Imidazole-M 2+ Complexes. Macromol Rapid Commun 2023; 44:e2300077. [PMID: 37337912 DOI: 10.1002/marc.202300077] [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: 03/16/2023] [Revised: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Histidine-M2+ coordination bonds are a recognized bond motif in biogenic materials with high hardness and extensibility, which has led to growing interest in their use in soft materials for mechanical function. However, the effect of different metal ions on the stability of the coordination complex remains poorly understood, complicating their implementation in metal-coordinated polymer materials. Herein, rheology experiments and density functional theory calculations are used to characterize the stability of coordination complexes and establish the binding hierarchy of histamine and imidazole with Ni2+ , Cu2+ , and Zn2+ . It is found that the binding hierarchy is driven by the specific affinity of the metal ions to different coordination states, which can be macroscopically tuned by changing the metal-to-ligand stoichiometry of the metal-coordinated network. These findings facilitate the rational selection of metal ions for optimizing the mechanical properties of metal-coordinated materials.
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Affiliation(s)
- Jake Song
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Eesha Khare
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Li Rao
- Department of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Niels Holten-Andersen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Bioengineering and Department of Materials Science and Engineering, Lehigh University, 27 Memorial Dr W, Bethlehem, PA, 18015, USA
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9
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Ravnik V, Jukič M, Bren U. Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach. J Chem Inf Model 2023; 63:5204-5219. [PMID: 37557084 PMCID: PMC10466382 DOI: 10.1021/acs.jcim.3c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Indexed: 08/11/2023]
Abstract
In order to identify the locations of metal ions in the binding sites of proteins, we have developed a method named the MADE (MAcromolecular DEnsity and Structure Analysis) approach. The MADE approach represents an evolution of our previous toolset, the ProBiS H2O (MD) methodology, for the identification of conserved water molecules. Our method uses experimental structures of proteins homologous to a query, which are subsequently superimposed upon it. Areas with a particular species present in a similar location among many homologous protein structures are identified using a clustering algorithm. Dense clusters likely represent positions containing species important to the query protein structure or function. We analyze well-characterized apo protein structures and show that the MADE approach can identify clusters corresponding to the expected positions of metal ions in their binding sites. The greatest advantage of our method lies in its generality. It can in principle be applied to any species found in protein records; it is not only limited to metal ions. We additionally demonstrate that the MADE approach can be successfully applied to predict the location of cofactors in computer-modeled structures, e.g., via AlphaFold. We also conduct a careful protein superposition method comparison and find our methodology robust and the results largely independent of the selected protein superposition algorithm. We postulate that with increasing structural data availability, additional applications of the MADE approach will be possible such as non-protein systems, water network identification, protein binding site elaboration, and analysis of binding events, all in a dynamic manner. We have implemented the MADE approach as a plugin for the PyMOL molecular visualization tool. The MADE plugin is available free of charge at https://gitlab.com/Jukic/made_software.
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Affiliation(s)
- Vid Ravnik
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova
ulica 17, Maribor SI-2000, Slovenia
| | - Marko Jukič
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova
ulica 17, Maribor SI-2000, Slovenia
- The
Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper SI-6000, Slovenia
- Institute
for Environmental Protection and Sensors, Beloruska ulica 7, Maribor SI-2000, Slovenia
| | - Urban Bren
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova
ulica 17, Maribor SI-2000, Slovenia
- The
Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper SI-6000, Slovenia
- Institute
for Environmental Protection and Sensors, Beloruska ulica 7, Maribor SI-2000, Slovenia
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10
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Tan H, Mao K, Cong X, Xin Y, Liu F, Wang J, Wang X, Han J, Zhang Y, Yang YG, Sun T. In Vivo Immune Adjuvant Effects of CaCO 3 Nanoparticles through Intracellular Ca 2+ Concentration Regulation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:39157-39166. [PMID: 37553750 DOI: 10.1021/acsami.3c07306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Calcium (Ca) is a vital component of the human body and plays a crucial role in intracellular signaling and regulation as a second messenger. Recent studies have shown that changes in intracellular Ca2+ concentration can influence immune cell function. In this study, we developed calcium carbonate nanoparticles (CaNPs) of various sizes using a Nanosystem Platform to modulate intracellular Ca2+ concentration in vitro and in vivo. Our findings demonstrate that intravenous administration of CaNPs led to changes in the number and ratio of immune cells in the spleen and stimulated the activation of dendritic cells (DCs) and macrophages. Notably, CaNPs exhibited strong adjuvant properties in the absence of antigenic stimuli. These results indicate that CaNPs have the potential to regulate immune cell function by modulating Ca2+ concentrations, offering a novel approach for disease prevention and treatment in combination with antigens or drugs. Overall, our study emphasizes the importance of modulating intracellular Ca2+ concentration as a means of regulating immune cell function.
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Affiliation(s)
- Huizhu Tan
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Kuirong Mao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- International Center of Future Science, Jilin University, Changchun, Jilin 130012, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Xiuxiu Cong
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Yanbao Xin
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Feiqi Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
| | - Jialiang Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Xin Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Jing Han
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Yuning Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Yong-Guang Yang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- International Center of Future Science, Jilin University, Changchun, Jilin 130012, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
| | - Tianmeng Sun
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, Jilin 130061, China
- International Center of Future Science, Jilin University, Changchun, Jilin 130012, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130062, China
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, Jilin 130012, China
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11
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Yuan Q, Chen S, Wang Y, Zhao H, Yang Y. Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning. Brief Bioinform 2022; 23:6770088. [PMID: 36274238 DOI: 10.1093/bib/bbac444] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/02/2022] [Accepted: 09/17/2022] [Indexed: 12/14/2022] Open
Abstract
More than one-third of the proteins contain metal ions in the Protein Data Bank. Correct identification of metal ion-binding residues is important for understanding protein functions and designing novel drugs. Due to the small size and high versatility of metal ions, it remains challenging to computationally predict their binding sites from protein sequence. Existing sequence-based methods are of low accuracy due to the lack of structural information, and time-consuming owing to the usage of multi-sequence alignment. Here, we propose LMetalSite, an alignment-free sequence-based predictor for binding sites of the four most frequently seen metal ions in BioLiP (Zn2+, Ca2+, Mg2+ and Mn2+). LMetalSite leverages the pretrained language model to rapidly generate informative sequence representations and employs transformer to capture long-range dependencies. Multi-task learning is adopted to compensate for the scarcity of training data and capture the intrinsic similarities between different metal ions. LMetalSite was shown to surpass state-of-the-art structure-based methods by more than 19.7, 14.4, 36.8 and 12.6% in area under the precision recall on the four independent tests, respectively. Further analyses indicated that the self-attention modules are effective to learn the structural contexts of residues from protein sequence. We provide the data sets, source codes and trained models of LMetalSite at https://github.com/biomed-AI/LMetalSite.
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Affiliation(s)
- Qianmu Yuan
- School of Computer Science and Engineering at Sun Yat-sen University, Guangzhou 510000, China
| | - Sheng Chen
- School of Computer Science and Engineering at Sun Yat-sen University, Guangzhou 510000, China
| | - Yu Wang
- Peng Cheng National Laboratory at Shenzhen, Guangzhou 510000, China
| | - Huiying Zhao
- Sun Yat-sen Memorial Hospital at Sun Yat-sen University, Guangzhou 510000, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China, and Key Laboratory of Machine Intelligence and Advanced Computing of MOE, Sun Yat-sen University, Guangzhou 510000, China
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12
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Marsden SR, Wijma HJ, Mohr MKF, Justo I, Hagedoorn P, Laustsen J, Jeffries CM, Svergun D, Mestrom L, McMillan DGG, Bento I, Hanefeld U. Substrate Induced Movement of the Metal Cofactor between Active and Resting State. Angew Chem Int Ed Engl 2022; 61:e202213338. [PMID: 36214476 PMCID: PMC10099721 DOI: 10.1002/anie.202213338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 11/11/2022]
Abstract
Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. In its resting state configuration (M2+ R ), the metal constitutes an integral part of the dimer interface within the overall hexameric assembly, but sterical constraints do not allow for substrate binding. Conversely, a second coordination sphere constitutes the catalytically active state (M2+ A ) at 2.4 Å distance. Bidentate coordination of a ketoacid substrate to M2+ A affords the overall lowest energy complex, which drives the transition from M2+ R to M2+ A . While not described earlier, this type of regulation may be widespread and largely overlooked due to low occupancy of some of its states in protein crystal structures.
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Affiliation(s)
- Stefan R. Marsden
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Hein J. Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute Faculty of Science and Engineering University of Groningen Nijenborg 4 9747AG Groningen The Netherlands
| | - Michael K. F. Mohr
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Inês Justo
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Peter‐Leon Hagedoorn
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | | | | | | | - Luuk Mestrom
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Duncan G. G. McMillan
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Isabel Bento
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Ulf Hanefeld
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
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13
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Cysteine driven decomposition and quenching of a fluorescent metalloreceptor: Optical detection and mechanistic insight. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Zhao Z, Ma Z, Wang B, Guan Y, Su XD, Jiang Z. Mn 2+ Directly Activates cGAS and Structural Analysis Suggests Mn 2+ Induces a Noncanonical Catalytic Synthesis of 2'3'-cGAMP. Cell Rep 2021; 32:108053. [PMID: 32814054 DOI: 10.1016/j.celrep.2020.108053] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
DNA binding allosterically activates the cytosolic DNA sensor cGAS (cyclic GMP-AMP [cGAMP] synthase) to synthesize 2'3'-cGAMP, using Mg2+ as the metal cofactor that catalyzes two nucleotidyl-transferring reactions. We previously found that Mn2+ potentiates cGAS activation, but the underlying mechanism remains unclear. Here, we report that Mn2+ directly activates cGAS. Structural analysis reveals that Mn2+-activated cGAS undergoes globally similar conformational changes to DNA-activated cGAS but forms a unique η1 helix to widen the catalytic pocket, allowing substrate entry and cGAMP synthesis. Strikingly, in Mn2+-activated cGAS, the linear intermediates pppGpG and pGpA take an inverted orientation in the active pocket, suggesting a noncanonical but accelerated cGAMP cyclization without substrate flip-over. Moreover, unlike the octahedral coordination around Mg2+, the two catalytic Mn2+ are coordinated by triphosphate moiety of the inverted substrate, independent of the catalytic triad residues. Our findings thus uncover Mn2+ as a cGAS activator that initiates noncanonical 2'3'-cGAMP synthesis.
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Affiliation(s)
- Zhen Zhao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhixing Ma
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Bo Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Yukun Guan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.
| | - Zhengfan Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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15
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Ramírez-Acosta S, Arias-Borrego A, Navarro-Roldán F, Selma-Royo M, Calatayud M, Collado MC, Huertas-Abril PV, Abril N, Barrera TG. Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review. Anal Chim Acta 2021; 1176:338620. [PMID: 34399890 DOI: 10.1016/j.aca.2021.338620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/12/2021] [Accepted: 04/01/2021] [Indexed: 02/08/2023]
Abstract
Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.
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Affiliation(s)
- Sara Ramírez-Acosta
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Ana Arias-Borrego
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Francisco Navarro-Roldán
- Department of Integrated Sciences, Cell Biology, Faculty of Experimental Sciences, University of Huelva, Spain
| | - Marta Selma-Royo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Marta Calatayud
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain.
| | - Tamara García Barrera
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain.
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16
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Rodríguez-Moro G, Ramírez-Acosta S, Callejón-Leblic B, Arias-Borrego A, García-Barrera T, Gómez-Ariza JL. Environmental metal toxicity assessment by the combined application of metallomics and metabolomics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25014-25034. [PMID: 33782823 DOI: 10.1007/s11356-021-13507-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The growing interest of our society for the environment, climate change, and the assurance of the quality of life and health has been the motor of new methodological proposals that allow a more comprehensive knowledge of the problems to be solved. In this sense, the potential of omic methodologies to study these problems from a global perspective represents a milestone in environmental studies. Therefore, the study of essential and toxic metals has a special interest, particularly in relation to toxicity issues and their association to biological interactions, transport, binding to biomolecules, and behavior in biological interfaces. These studies have promoted new instrumental platforms and methodological approaches that allow addressing these problems. Furthermore, to encompass the reality of molecule-atoms interactions in their completeness, combinations of omics have been tried, focusing on environment, food, and health issues. In this sense, the present work is situated, with the objective of reviewing the most recent methodological proposals in the field of the environment and their applications, considering not only the analytical approaches but also how they have to be applied, the use of bioindicators' exposure experiments in the laboratory, and the potential transfer of the findings from the laboratory to the field. This latter point is a true touchstone, which makes these new analytical methodologies in the necessary tools for understanding the environment and the consequences of its imbalance.
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Affiliation(s)
- Gema Rodríguez-Moro
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Huelva, Spain
- International Agrofood Campus of Excellence International ceiA3, University of Huelva, Huelva, Spain
- Research Center of Natural Resources, Health and the Environment (RENSMA), University of Huelva, Huelva, Spain
| | - Sara Ramírez-Acosta
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Huelva, Spain
- International Agrofood Campus of Excellence International ceiA3, University of Huelva, Huelva, Spain
- Research Center of Natural Resources, Health and the Environment (RENSMA), University of Huelva, Huelva, Spain
| | - Belén Callejón-Leblic
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Huelva, Spain
- International Agrofood Campus of Excellence International ceiA3, University of Huelva, Huelva, Spain
- Research Center of Natural Resources, Health and the Environment (RENSMA), University of Huelva, Huelva, Spain
| | - Ana Arias-Borrego
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Huelva, Spain
- International Agrofood Campus of Excellence International ceiA3, University of Huelva, Huelva, Spain
- Research Center of Natural Resources, Health and the Environment (RENSMA), University of Huelva, Huelva, Spain
| | - Tamara García-Barrera
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Huelva, Spain.
- International Agrofood Campus of Excellence International ceiA3, University of Huelva, Huelva, Spain.
- Research Center of Natural Resources, Health and the Environment (RENSMA), University of Huelva, Huelva, Spain.
| | - José-Luis Gómez-Ariza
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Huelva, Spain.
- International Agrofood Campus of Excellence International ceiA3, University of Huelva, Huelva, Spain.
- Research Center of Natural Resources, Health and the Environment (RENSMA), University of Huelva, Huelva, Spain.
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17
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Gamble Jarvi A, Bogetti X, Singewald K, Ghosh S, Saxena S. Going the dHis-tance: Site-Directed Cu 2+ Labeling of Proteins and Nucleic Acids. Acc Chem Res 2021; 54:1481-1491. [PMID: 33476119 DOI: 10.1021/acs.accounts.0c00761] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this Account, we showcase site-directed Cu2+ labeling in proteins and DNA, which has opened new avenues for the measurement of the structure and dynamics of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. In proteins, the spin label is assembled in situ from natural amino acid residues and a metal complex and requires no post-expression synthetic modification or purification procedures. The labeling scheme exploits a double histidine (dHis) motif, which utilizes endogenous or site-specifically mutated histidine residues to coordinate a Cu2+ complex. Pulsed EPR measurements on such Cu2+-labeled proteins potentially yield distance distributions that are up to 5 times narrower than the common protein spin label-the approach, thus, overcomes the inherent limitation of the current technology, which relies on a spin label with a highly flexible side chain. This labeling scheme provides a straightforward method that elucidates biophysical information that is costly, complicated, or simply inaccessible by traditional EPR labels. Examples include the direct measurement of protein backbone dynamics at β-sheet sites, which are largely inaccessible through traditional spin labels, and rigid Cu2+-Cu2+ distance measurements that enable higher precision in the analysis of protein conformations, conformational changes, interactions with other biomolecules, and the relative orientations of two labeled protein subunits. Likewise, a Cu2+ label has been developed for use in DNA, which is small, is nucleotide independent, and is positioned within the DNA helix. The placement of the Cu2+ label directly reports on the biologically relevant backbone distance. Additionally, for both of these labeling techniques, we have developed models for interpretation of the EPR distance information, primarily utilizing molecular dynamics (MD) simulations. Initial results using force fields developed for both protein and DNA labels have agreed with experimental results, which has been a major bottleneck for traditional spin labels. Looking ahead, we anticipate new combinations of MD and EPR to further our understanding of protein and DNA conformational changes, as well as working synergistically to investigate protein-DNA interactions.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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18
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Matsarskaia O, Roosen‐Runge F, Schreiber F. Multivalent ions and biomolecules: Attempting a comprehensive perspective. Chemphyschem 2020; 21:1742-1767. [PMID: 32406605 PMCID: PMC7496725 DOI: 10.1002/cphc.202000162] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.
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Affiliation(s)
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and SocietyMalmö UniversitySweden
- Division of Physical ChemistryLund UniversitySweden
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19
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Alnahwi A, Ait-Mohand S, Dumulon-Perreault V, Dory YL, Guérin B. Promising Performance of 4HMS, a New Zirconium-89 Octadendate Chelator. ACS OMEGA 2020; 5:10731-10739. [PMID: 32455192 PMCID: PMC7240819 DOI: 10.1021/acsomega.0c00207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Over the last decade, the interest in zirconium-89 (89Zr) as a positron-emitting radionuclide increased considerably because of its standardized production and its physical half-life (78.41 h), which matches the biological half-life of antibodies and its successful use in preclinical and clinical applications. So far, desferrioxamine (DFO), a commercially available chelator, has been mainly used as a bifunctional chelating system. However, there are some concerns regarding the in vivo stability of the [89Zr]Zr-DFO complex. In this study, we report the synthesis of an acyclic N-hydroxy-N-methyl succinamide-based chelator (4HMS) with 8 coordination sites and our first investigations into the use of this new chelator for 89Zr complexation. In vitro and in vivo comparative studies with [89Zr]Zr-4HMS and [89Zr]Zr-DFO are presented. The 4HMS chelator was synthesized in four steps starting with an excellent overall yield. Both chelators were quantitatively labeled with 89Zr within 5-10 min at pH 7 and room temperature; the molar activity of [89Zr]Zr-4HMS exceeded (>3 times) that of [89Zr]Zr-DFO. [89Zr]Zr-4HMS remained stable against transmetalation and transchelation and cleared from most tissues within 24 h. The kidney, liver, bone, and spleen uptakes were significantly low for this 89Zr-complex. Positron emission tomography images were in accordance with the results of the biodistribution in healthy mice. Based on DFT calculations, a rationale is provided for the high stability of 89Zr-4HMS. This makes 4HMS a promising chelator for future development of 89Zr-radiopharmaceuticals.
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Affiliation(s)
- Aiman
H. Alnahwi
- Department
of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Samia Ait-Mohand
- Department
of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Véronique Dumulon-Perreault
- Sherbrooke
Molecular Imaging Center (CIMS), CRCHUS, 3001, 12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Yves L. Dory
- Laboratoire
de Synthèse Supramoléculaire. Department of Chemistry,
Institut de Pharmacologie, Université
de Sherbooke, 3001, 12e
Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Brigitte Guérin
- Department
of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
- Sherbrooke
Molecular Imaging Center (CIMS), CRCHUS, 3001, 12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
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20
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Hu X, Feng Z, Zhang X, Liu L, Wang S. The Identification of Metal Ion Ligand-Binding Residues by Adding the Reclassified Relative Solvent Accessibility. Front Genet 2020; 11:214. [PMID: 32265982 PMCID: PMC7096583 DOI: 10.3389/fgene.2020.00214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/24/2020] [Indexed: 11/13/2022] Open
Abstract
Many proteins realize their special functions by binding with specific metal ion ligands during a cell's life cycle. The ability to correctly identify metal ion ligand-binding residues is valuable for the human health and the design of molecular drug. Precisely identifying these residues, however, remains challenging work. We have presented an improved computational approach for predicting the binding residues of 10 metal ion ligands (Zn2+, Cu2+, Fe2+, Fe3+, Co2+, Ca2+, Mg2+, Mn2+, Na+, and K+) by adding reclassified relative solvent accessibility (RSA). The best accuracy of fivefold cross-validation was higher than 77.9%, which was about 16% higher than the previous result on the same dataset. It was found that different reclassification of the RSA information can make different contributions to the identification of specific ligand binding residues. Our study has provided an additional understanding of the effect of the RSA on the identification of metal ion ligand binding residues.
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Affiliation(s)
| | - Zhenxing Feng
- College of Sciences, Inner Mongolla University of Technology, Hohhot, China
| | - Xiaojin Zhang
- College of Sciences, Inner Mongolla University of Technology, Hohhot, China
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21
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Disruption of the Metal Ion Environment by EDTA for Silk Formation Affects the Mechanical Properties of Silkworm Silk. Int J Mol Sci 2019; 20:ijms20123026. [PMID: 31234286 PMCID: PMC6627089 DOI: 10.3390/ijms20123026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/16/2019] [Accepted: 06/16/2019] [Indexed: 11/22/2022] Open
Abstract
Silk fiber has become a research focus because of its comprehensive mechanical properties. Metal ions can influence the conformational transition of silk fibroin. Current research is mainly focused on the role of a single ion, rather than the whole metal ion environment. Here, we report the effects of the overall metal ion environment on the secondary structure and mechanical properties of silk fibers after direct injection and feeding of silkworms with EDTA. The metal composition of the hemolymph, silk gland, and silk fiber changed significantly post EDTA treatment. Synchrotron FTIR analysis indicated that the secondary structure of silk fiber after EDTA treatment changed dramatically; particularly, the β-sheets decreased and the β-turns increased. Post EDTA treatment, the silk fiber had significantly decreased strength, Young’s modulus, and toughness as compared with the control groups, while the strain exhibited no obvious change. These changes can be attributed to the change in the metal ion environment in the silk fibroin and sericin in the silk gland. Our investigation provides a new theoretical basis for the natural silk spinning process, and our findings could help develop a method to modify the mechanical properties of silk fiber using metal ions.
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22
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Callejón-Leblic B, Arias-Borrego A, Pereira-Vega A, Gómez-Ariza JL, García-Barrera T. The Metallome of Lung Cancer and its Potential Use as Biomarker. Int J Mol Sci 2019; 20:ijms20030778. [PMID: 30759767 PMCID: PMC6387380 DOI: 10.3390/ijms20030778] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Carcinogenesis is a very complex process in which metals have been found to be critically involved. In this sense, a disturbed redox status and metal dyshomeostasis take place during the onset and progression of cancer, and it is well-known that trace elements participate in the activation or inhibition of enzymatic reactions and metalloproteins, in which they usually participate as cofactors. Until now, the role of metals in cancer have been studied as an effect, establishing that cancer onset and progression affects the disturbance of the natural chemical form of the essential elements in the metabolism. However, it has also been studied as a cause, giving insights related to the high exposure of metals giving a place to the carcinogenic process. On the other hand, the chemical species of the metal or metallobiomolecule is very important, since it finally affects the biological activity or the toxicological potential of the element and their mobility across different biological compartments. Moreover, the importance of metal homeostasis and metals interactions in biology has also been demonstrated, and the ratios between some elements were found to be different in cancer patients; however, the interplay of elements is rarely reported. This review focuses on the critical role of metals in lung cancer, which is one of the most insidious forms of cancer, with special attention to the analytical approaches and pitfalls to extract metals and their species from tissues and biofluids, determining the ratios of metals, obtaining classification profiles, and finally defining the metallome of lung cancer.
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Affiliation(s)
- Belén Callejón-Leblic
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Research Center on Health and Environment (RENSMA), 21007 Huelva, Spain.
| | - Ana Arias-Borrego
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Research Center on Health and Environment (RENSMA), 21007 Huelva, Spain.
| | | | - José Luis Gómez-Ariza
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Research Center on Health and Environment (RENSMA), 21007 Huelva, Spain.
| | - Tamara García-Barrera
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus de El Carmen, Research Center on Health and Environment (RENSMA), 21007 Huelva, Spain.
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Gamble Jarvi A, Cunningham TF, Saxena S. Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements. Phys Chem Chem Phys 2019; 21:10238-10243. [DOI: 10.1039/c8cp07143h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu2+ labeling and long range distance measurements by EPR.
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Affiliation(s)
| | | | - Sunil Saxena
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
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24
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Almhjell PJ, Mills JH. Metal-chelating non-canonical amino acids in metalloprotein engineering and design. Curr Opin Struct Biol 2018; 51:170-176. [DOI: 10.1016/j.sbi.2018.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/12/2018] [Indexed: 11/26/2022]
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25
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Li S, Wang J, Zhang B, Liu Y, Lu T, Shi Y, Shan G, Dong L. Urinary Lead Concentration Is an Independent Predictor of Cancer Mortality in the U.S. General Population. Front Oncol 2018; 8:242. [PMID: 30013948 PMCID: PMC6036403 DOI: 10.3389/fonc.2018.00242] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Lead is a ubiquitous pollutant that constitutes an environmental hazard worldwide. Although lead has been known as a carcinogenic factor in animal models, its role in human carcinogenesis is still a topic of debate with limited epidemiological evidence. Moreover, the association between urinary lead, as the most non-invasive and accessible way for lead measurement in human, and cancer mortality in general population has never been explored. We addressed this subject using continuous National Health and Nutrition Examination Survey 1999-2010 data and its Mortality Follow-Up Study. Of 5,316 subjects in study population, 161 participants died due to cancer. Cancer-specific mortality was associated with urinary lead levels after multivariable adjustment. Kaplan-Meier survival curve and cubic regression spline analyses indicated that high concentration of urinary lead exhibited significant association with raised death rate of cancer. Despite the marked decrease in environmental lead levels over the past three decades, lead exposure is still the significant determinant of cancer mortality in general population in U.S., and quantification of urinary lead may serve as a non-invasive approach to facilitate biomarker discovery and clinical translational research.
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Affiliation(s)
- Sen Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
- Department of Physiology, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Jiaxin Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Biao Zhang
- Department of Epidemiology and Statistics, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Liu
- Department of Biostatistics and Bioinformatics, Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Tao Lu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuanyuan Shi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Guangliang Shan
- Department of Epidemiology and Statistics, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Dong
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
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26
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A Diversified Spectrometric and Molecular Docking Technique to Biophysical Study of Interaction between Bovine Serum Albumin and Sodium Salt of Risedronic Acid, a Bisphosphonate for Skeletal Disorders. Bioinorg Chem Appl 2018; 2018:6954951. [PMID: 30050563 PMCID: PMC6046188 DOI: 10.1155/2018/6954951] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 05/10/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
The binding interaction between bovine serum albumin (BSA) and sodium salt of risedronic acid (RSN) was studied by using the FT-IR (Fourier transform infrared), UV-Vis (ultraviolet–visible), fluorescence (emission and synchronous), CD (circular dichroism) spectrometric, and computational (molecular docking) techniques at 289, 297, and 305 K temperatures with physiological buffer of pH 7.40. The conformational and secondary structural changes observed for BSA from CD spectra and by curve fitting procedure were applied to Fourier self-deconvolution in FT-IR spectra. The formation of a BSA-RSN complex was confirmed from UV-Vis spectroscopy. The static type of quenching shown for RSN to BSA was verified from Stern–Volmer and modified Stern–Volmer equations. The binding constant of order 105 was obtained to be confirming that there exists a strong binding interaction between BSA and RSN. Synchronous fluorescence shows that the microenvironment of tryptophan was altered, not tyrosine of BSA; in addition to this, the distance between tryptophan of BSA and RSN was found out from Forster's theory of nonradiation energy transfer. The interaction between BSA and RSN mainly occurred as a result of hydrogen bonds and van der Waals forces, the process is exothermic and spontaneous, and it was achieved through van 't Hoff equation. This interaction was affected by the presence of biologically active Fe2+, Ni2+, Ca2+, Mg2+, and Cd2+ ions and was also studied. The subdomain IIIA of BSA involved with RSN interaction was authenticated from molecular docking analysis.
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27
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García-Barrera T, Rodríguez-Moro G, Callejón-Leblic B, Arias-Borrego A, Gómez-Ariza J. Mass spectrometry based analytical approaches and pitfalls for toxicometabolomics of arsenic in mammals: A tutorial review. Anal Chim Acta 2018; 1000:41-66. [DOI: 10.1016/j.aca.2017.10.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/18/2017] [Accepted: 10/21/2017] [Indexed: 02/06/2023]
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28
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Uribe L, Diezemann G, Gauss J, Morth JP, Cascella M. Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations. Chemistry 2018; 24:5074-5077. [PMID: 29243856 DOI: 10.1002/chem.201705159] [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: 10/31/2017] [Indexed: 01/15/2023]
Abstract
We performed quantum-chemical calculations, ab initio molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) and enhanced sampling metadynamics simulations to investigate the origin of metal specificity in isatin hydrolase from Labrenzia aggregata. The peculiar octahedral binding geometry of the Mn2+ ion in the Michaelis complex includes both the isatin substrate and the catalytic water within the first coordination shell of the cation. Our calculations show that the same arrangement of the ligands cannot be efficiently achieved in the presence of other small divalent metal cations such as Zn2+ or Cu2+ . On the contrary, bulkier alkaline-earth cations such as Mg2+ , which allow octahedral coordination, are not able to activate the catalytic water into the stronger OH- nucleophile required to attack the stable N-aryl-amide moiety of isatin.
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Affiliation(s)
- Lalita Uribe
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Graduate School Materials Science in Mainz, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128, Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Jens Preben Morth
- Norwegian Centre for Molecular Medicine, Nordic EMBL Partnership, University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital, Ullevål, PO Box 4965 Nydalen, 0424, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular, Sciences, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
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29
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Rodríguez-Moro G, Ramírez-Acosta S, Arias-Borrego A, García-Barrera T, Gómez-Ariza JL. Environmental Metallomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1055:39-66. [DOI: 10.1007/978-3-319-90143-5_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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30
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Kumar S. Prediction of Metal Ion Binding Sites in Proteins from Amino Acid Sequences by Using Simplified Amino Acid Alphabets and Random Forest Model. Genomics Inform 2017; 15:162-169. [PMID: 29307143 PMCID: PMC5769865 DOI: 10.5808/gi.2017.15.4.162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 11/20/2022] Open
Abstract
Metal binding proteins or metallo-proteins are important for the stability of the protein and also serve as co-factors in various functions like controlling metabolism, regulating signal transport, and metal homeostasis. In structural genomics, prediction of metal binding proteins help in the selection of suitable growth medium for overexpression's studies and also help in obtaining the functional protein. Computational prediction using machine learning approach has been widely used in various fields of bioinformatics based on the fact all the information contains in amino acid sequence. In this study, random forest machine learning prediction systems were deployed with simplified amino acid for prediction of individual major metal ion binding sites like copper, calcium, cobalt, iron, magnesium, manganese, nickel, and zinc.
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Affiliation(s)
- Suresh Kumar
- Department of Diagnostic and Allied Health Sciences, Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Malaysia
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31
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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32
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33
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Cao X, Hu X, Zhang X, Gao S, Ding C, Feng Y, Bao W. Identification of metal ion binding sites based on amino acid sequences. PLoS One 2017; 12:e0183756. [PMID: 28854211 PMCID: PMC5576659 DOI: 10.1371/journal.pone.0183756] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/10/2017] [Indexed: 11/26/2022] Open
Abstract
The identification of metal ion binding sites is important for protein function annotation and the design of new drug molecules. This study presents an effective method of analyzing and identifying the binding residues of metal ions based solely on sequence information. Ten metal ions were extracted from the BioLip database: Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+ and Co2+. The analysis showed that Zn2+, Cu2+, Fe2+, Fe3+, and Co2+ were sensitive to the conservation of amino acids at binding sites, and promising results can be achieved using the Position Weight Scoring Matrix algorithm, with an accuracy of over 79.9% and a Matthews correlation coefficient of over 0.6. The binding sites of other metals can also be accurately identified using the Support Vector Machine algorithm with multifeature parameters as input. In addition, we found that Ca2+ was insensitive to hydrophobicity and hydrophilicity information and Mn2+ was insensitive to polarization charge information. An online server was constructed based on the framework of the proposed method and is freely available at http://60.31.198.140:8081/metal/HomePage/HomePage.html.
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Affiliation(s)
- Xiaoyong Cao
- College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Xiuzhen Hu
- College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Xiaojin Zhang
- College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Sujuan Gao
- College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051, China
- College of Sciences, Inner Mongolia Agricultural University, Hohhot, 010021, China
| | - Changjiang Ding
- College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Yonge Feng
- College of Sciences, Inner Mongolia Agricultural University, Hohhot, 010021, China
| | - Weihua Bao
- College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051, China
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34
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Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 500] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
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Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
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35
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Escobar S, Velasco-Lozano S, Lu CH, Lin YF, Mesa M, Bernal C, López-Gallego F. Understanding the functional properties of bio-inorganic nanoflowers as biocatalysts by deciphering the metal-binding sites of enzymes. J Mater Chem B 2017; 5:4478-4486. [PMID: 32263975 DOI: 10.1039/c6tb03295h] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biomineralisation of metal phosphates is a promising approach to develop more efficient nanobiocatalysts; however, the interactions between the protein and the inorganic mineral are poorly understood. Elucidating which protein regions most likely participate in the mineral formation will guide the fabrication of more efficient biocatalysts based on metal-phosphate nanoflowers. We have biomineralised the lipase from Thermomyces lanuginosus using three calcium, zinc and copper phosphates to fabricate different types of bio-inorganic nanoflowers. To better understand how the biomineralisation process affects the enzyme properties, we have computationally predicted the protein regions with a higher propensity for binding Ca2+, Cu2+ and Zn2+. These binding sites can be considered as presumable nucleation points where the biomineralisation process starts and explain why different metals can form bio-inorganic nanoflowers of the same enzyme with different functional properties. The formation of calcium, copper and zinc phosphates in the presence of this lipase gives rise to nanoflowers with different morphologies and different enzymatic properties such as activity, stability, hyperactivation and activity-pH profile; these functional differences are supported by structural studies based on fluorescence spectroscopy and can be explained by the different locations of the predicted nucleation sites for the different metals. Among the three metals used herein, the mineralisation of this lipase with zinc-phosphate enables the fabrication of bio-inorganic nanoflowers 34 times more stable than the soluble enzyme. These bio-inorganic nanoflowers were reused for 8 reaction cycles achieving 100% yield in the hydrolysis of p-nitrophenol butyrate but losing more than 50% of their initial activity after 6 operational cycles. Finally, this heterogeneous biocatalyst was more active and enantioselective than the soluble enzyme (ee = 79%(R)) towards the kinetic resolution of rac-1-phenylethyl acetate yielding the R enantiomer with ee = 84%.
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Affiliation(s)
- Sindy Escobar
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia - UdeA, Calle 70 No. 52-21, Medellín, Colombia
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36
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Zhu SY, Li XN, Sun XC, Lin J, Li W, Zhang C, Li JL. Biochemical characterization of the selenoproteome in Gallus gallus via bioinformatics analysis: structure–function relationships and interactions of binding molecules. Metallomics 2017; 9:124-131. [DOI: 10.1039/c6mt00254d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Dutta Gupta D, Usharani D, Mazumdar S. Mono-nuclear copper complexes mimicking the intermediates for the binuclear copper center of the subunit II of cytochrome oxidase: a peptide based approach. Dalton Trans 2016; 45:17624-17632. [PMID: 27747364 DOI: 10.1039/c6dt02977a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three stable copper complexes of peptides derived from the copper ion binding loop of the subunit II of cytochrome c oxidase have been prepared and characterized by various spectroscopic techniques. These stable copper complexes of peptides were found to exhibit cysteine, histidine and/or methionine ligation, which has predominant σ-contribution in the Cys-Cu charge transfer. The copper(ii) peptide complexes showed type-2 EPR spectra, which is uncommon in copper-cysteinate complexes. UV-visible spectra, Raman and EPR results support a tetragonal structure of the coordination geometry around the copper ion. The copper complex of the 9-amino acid peptide suggested the formation of a 'red' copper center while the copper complexes of the 12- and 11-amino acid peptides showed the formation of a 'green' copper center. The results provide insights on the first stable models of the copper complexes formed in the peptide scaffold that mimic the mono-nuclear copper bound protein intermediates proposed during the formation of the binuclear Cu2S2 core of the enzyme. These three copper complexes of peptides derived from the metal ion binding loop of the CuA center of the subunit II of cytochrome c oxidase showed novel spectroscopic properties which have not so far been reported in any stable small complex.
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Affiliation(s)
- Dwaipayan Dutta Gupta
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India.
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38
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Pascolo L, Gianoncelli A, Rizzardi C, de Jonge M, Howard D, Paterson D, Cammisuli F, Salomé M, De Paoli P, Melato M, Canzonieri V. Focused X-Ray Histological Analyses to Reveal Asbestos Fibers and Bodies in Lungs and Pleura of Asbestos-Exposed Subjects. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:1062-1071. [PMID: 27619825 DOI: 10.1017/s1431927616011685] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Asbestos bodies are the histological hallmarks of asbestos exposure. Both conventional and advanced techniques are used to evaluate abundance and composition in histological samples. We previously reported the possibility of using synchrotron X-ray fluorescence microscopy (XFM) for analyzing the chemical composition of asbestos bodies directly in lung tissue samples. Here we applied a high-performance synchrotron X-ray fluorescence (XRF) set-up that could allow new protocols for fast monitoring of the occurrence of asbestos bodies in large histological sections, improving investigation of the related chemical changes. A combination of synchrotron X-ray transmission and fluorescence microscopy techniques at different energies at three distinct synchrotrons was used to characterize asbestos in paraffinated lung tissues. The fast chemical imaging of the XFM beamline (Australian Synchrotron) demonstrates that asbestos bodies can be rapidly and efficiently identified as co-localization of high calcium and iron, the most abundant elements of these formations inside tissues (Fe up to 10% w/w; Ca up to 1%). By following iron presence, we were also able to hint at small asbestos fibers in pleural spaces. XRF at lower energy and at higher spatial resolution was afterwards performed to better define small fibers. These analyses may predispose for future protocols to be set with laboratory instruments.
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Affiliation(s)
- Lorella Pascolo
- 1Department of Medical, Surgical, and Health Sciences,University of Trieste,34149 Trieste,Italy
| | | | - Clara Rizzardi
- 1Department of Medical, Surgical, and Health Sciences,University of Trieste,34149 Trieste,Italy
| | - Martin de Jonge
- 3Australian Synchrotron,3168 Clayton,Melbourne,VIC,Australia
| | - Daryl Howard
- 3Australian Synchrotron,3168 Clayton,Melbourne,VIC,Australia
| | - David Paterson
- 3Australian Synchrotron,3168 Clayton,Melbourne,VIC,Australia
| | - Francesca Cammisuli
- 1Department of Medical, Surgical, and Health Sciences,University of Trieste,34149 Trieste,Italy
| | - Murielle Salomé
- 4European Synchrotron Radiation Facility,38000 Grenoble,Cedex 9,France
| | - Paolo De Paoli
- 5Scientific Direction,Centro di Riferimento Oncologico (CRO),National Cancer Institute,IRCCS,33081 Aviano (PN),Italy
| | - Mauro Melato
- 6Institute for Maternal and Child Health,IRCCS Burlo Garofolo,34137 Trieste,Italy
| | - Vincenzo Canzonieri
- 7Division of Pathology,Centro di Riferimento Oncologico (CRO),National Cancer Institute,IRCCS,33081 Aviano (PN),Italy
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Lin JM, Tsai YT, Liu YH, Lin Y, Tai HC, Chen CS. Identification of 2-oxohistidine Interacting Proteins Using E. coli Proteome Chips. Mol Cell Proteomics 2016; 15:3581-3593. [PMID: 27644758 DOI: 10.1074/mcp.m116.060806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/26/2016] [Indexed: 11/06/2022] Open
Abstract
Cellular proteins are constantly damaged by reactive oxygen species generated by cellular respiration. Because of its metal-chelating property, the histidine residue is easily oxidized in the presence of Cu/Fe ions and H2O2 via metal-catalyzed oxidation, usually converted to 2-oxohistidine. We hypothesized that cells may have evolved antioxidant defenses against the generation of 2-oxohistidine residues on proteins, and therefore there would be cellular proteins which specifically interact with this oxidized side chain. Using two chemically synthesized peptide probes containing 2-oxohistidine, high-throughput interactome screening was conducted using the E. coli K12 proteome microarray containing >4200 proteins. Ten interacting proteins were identified, and successfully validated using a third peptide probe, fluorescence polarization assays, as well as binding constant measurements. We discovered that 9 out of 10 identified proteins seemed to be involved in redox-related cellular functions. We also built the functional interaction network to reveal their interacting proteins. The network showed that our interacting proteins were enriched in oxido-reduction processes, ion binding, and carbon metabolism. A consensus motif was identified among these 10 bacterial interacting proteins based on bioinformatic analysis, which also appeared to be present on human S100A1 protein. Besides, we found that the consensus binding motif among our identified proteins, including bacteria and human, were located within α-helices and faced the outside of proteins. The combination of chemically engineered peptide probes with proteome microarrays proves to be an efficient discovery platform for protein interactomes of unusual post-translational modifications, and sensitive enough to detect even the insertion of a single oxygen atom in this case.
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Affiliation(s)
- Jun-Mu Lin
- From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan.,§Department of Biomedical Sciences and Engineering, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan
| | - Yu-Ting Tsai
- ¶Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yu-Hsuan Liu
- ¶Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yun Lin
- ¶Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Hwan-Ching Tai
- ¶Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chien-Sheng Chen
- From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan; .,§Department of Biomedical Sciences and Engineering, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan
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40
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Hu X, Dong Q, Yang J, Zhang Y. Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. ACTA ACUST UNITED AC 2016; 32:3260-3269. [PMID: 27378301 DOI: 10.1093/bioinformatics/btw396] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/18/2016] [Indexed: 11/13/2022]
Abstract
MOTIVATION More than half of proteins require binding of metal and acid radical ions for their structure and function. Identification of the ion-binding locations is important for understanding the biological functions of proteins. Due to the small size and high versatility of the metal and acid radical ions, however, computational prediction of their binding sites remains difficult. RESULTS We proposed a new ligand-specific approach devoted to the binding site prediction of 13 metal ions (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+) and acid radical ion ligands (CO32-, NO2-, SO42-, PO43-) that are most frequently seen in protein databases. A sequence-based ab initio model is first trained on sequence profiles, where a modified AdaBoost algorithm is extended to balance binding and non-binding residue samples. A composite method IonCom is then developed to combine the ab initio model with multiple threading alignments for further improving the robustness of the binding site predictions. The pipeline was tested using 5-fold cross validations on a comprehensive set of 2,100 non-redundant proteins bound with 3,075 small ion ligands. Significant advantage was demonstrated compared with the state of the art ligand-binding methods including COACH and TargetS for high-accuracy ion-binding site identification. Detailed data analyses show that the major advantage of IonCom lies at the integration of complementary ab initio and template-based components. Ion-specific feature design and binding library selection also contribute to the improvement of small ion ligand binding predictions. AVAILABILITY AND IMPLEMENTATION http://zhanglab.ccmb.med.umich.edu/IonCom CONTACT: hxz@imut.edu.cn or zhng@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiuzhen Hu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA College of Sciences, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Qiwen Dong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA Institute for Data Science and Engineering, East China Normal University, Shanghai 200062, China
| | - Jianyi Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA School of Mathematical Sciences, Nankai University, Tianjin 300071, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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41
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Lee HS, Im W. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design. Protein Sci 2016; 25:865-76. [PMID: 26813336 DOI: 10.1002/pro.2890] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/11/2022]
Abstract
Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/.
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Affiliation(s)
- Hui Sun Lee
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, University of Kansas, Lawrence, Kansas, 66047
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42
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Colombo M, Girard E, Franzetti B. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites. Sci Rep 2016; 6:20876. [PMID: 26853450 PMCID: PMC4745047 DOI: 10.1038/srep20876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/11/2016] [Indexed: 11/09/2022] Open
Abstract
TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn(2+), hyperthermophilic TETs prefers Co(2+). Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites.
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Affiliation(s)
- Matteo Colombo
- CNRS, IBS, F-38027 Grenoble, France.,CEA, DSV, IBS, F-38027 Grenoble, France.,Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Eric Girard
- CNRS, IBS, F-38027 Grenoble, France.,CEA, DSV, IBS, F-38027 Grenoble, France.,Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Bruno Franzetti
- CNRS, IBS, F-38027 Grenoble, France.,CEA, DSV, IBS, F-38027 Grenoble, France.,Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
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43
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Urinary metallomics as a novel biomarker discovery platform: Breast cancer as a case study. Clin Chim Acta 2016; 452:142-8. [DOI: 10.1016/j.cca.2015.11.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 11/18/2022]
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44
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Bengtsson G, Pallon J, Nilsson C, Triebskorn R, Köhler HR. PIXE-electrophoresis shows starving collembolan reallocates protein-bound metals. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:115-120. [PMID: 26507895 DOI: 10.1007/s10646-015-1573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
One of multiple functions of metalloproteins is to provide detoxification to excess metal levels in organisms. Here we address the induction and persistence of a range of low to high molecular weight copper- and zinc binding proteins in the collembolan species Tetrodontophora bielanensis exposed to copper- and zinc-enriched food, followed by a period of recovery from metal exposure, in absence and presence of food. After 10 days of feeding copper and zinc contaminated yeast, specimens were either moved to ample of leaf litter material from their woodland stand of origin or starved (no food offered). The molecular weight distribution of metal binding proteins was determined by native polyacryl gel electrophoresis. One gel was stained with Comassie brilliant blue and a duplicate gel dried and scanned for the amount of copper and zinc by particle-induced X-ray emission. Specimens exposed to copper and recovered from it with ample of food had copper bound to two groups of rather low molecular weight proteins (40-50 kDa) and two of intermediate size (70-80 kDa). Most zinc in specimens from the woodland stand was bound to two large proteins of about 104 and 106 kDa. The same proteins were holding some zinc in metal-exposed specimens, but most zinc was found in proteins <40 kDa in size. Specimens recovered from metal exposure in presence of ample of food had the same distribution pattern of zinc binding proteins, whereas starved specimens had zinc as well as copper mainly bound to two proteins of 8 and 10 kDa in size. Thus, the induction and distribution of copper- and zinc-binding proteins depend on exposure conditions, and the presence of low molecular weight binding proteins, characteristic of metallothioneins, was mainly limited to starving conditions.
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Affiliation(s)
- Göran Bengtsson
- Department of Ecology, University of Lund, Sölvegatan 37, 22362, Lund, Sweden.
| | - Jan Pallon
- Department of Nuclear Physics, Lund Institute of Technology, Sölvegatan 14, 22362, Lund, Sweden
| | - Christina Nilsson
- Department of Nuclear Physics, Lund Institute of Technology, Sölvegatan 14, 22362, Lund, Sweden
| | - Rita Triebskorn
- Animal Physiological Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
- Transfer Center Ecotoxicology and Ecophysiology, Blumenstrasse 13, 72108, Rottenburg, Germany
| | - Heinz-R Köhler
- Animal Physiological Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
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45
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Hagedoorn PL. Microbial Metalloproteomics. Proteomes 2015; 3:424-439. [PMID: 28248278 PMCID: PMC5217388 DOI: 10.3390/proteomes3040424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP)-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
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46
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Fuss JO, Tsai CL, Ishida JP, Tainer JA. Emerging critical roles of Fe-S clusters in DNA replication and repair. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1853:1253-71. [PMID: 25655665 PMCID: PMC4576882 DOI: 10.1016/j.bbamcr.2015.01.018] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Fe-S clusters are partners in the origin of life that predate cells, acetyl-CoA metabolism, DNA, and the RNA world. The double helix solved the mystery of DNA replication by base pairing for accurate copying. Yet, for genome stability necessary to life, the double helix has equally important implications for damage repair. Here we examine striking advances that uncover Fe-S cluster roles both in copying the genetic sequence by DNA polymerases and in crucial repair processes for genome maintenance, as mutational defects cause cancer and degenerative disease. Moreover, we examine an exciting, controversial role for Fe-S clusters in a third element required for life - the long-range coordination and regulation of replication and repair events. By their ability to delocalize electrons over both Fe and S centers, Fe-S clusters have unbeatable features for protein conformational control and charge transfer via double-stranded DNA that may fundamentally transform our understanding of life, replication, and repair. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Jill O Fuss
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Chi-Lin Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Justin P Ishida
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.
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47
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García-Sevillano M, Rodríguez-Moro G, García-Barrera T, Navarro F, Gómez-Ariza J. Biological interactions between mercury and selenium in distribution and detoxification processes in mice under controlled exposure. Effects on selenoprotein. Chem Biol Interact 2015; 229:82-90. [DOI: 10.1016/j.cbi.2015.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/24/2015] [Accepted: 02/01/2015] [Indexed: 02/06/2023]
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48
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Huang CF, Liu YH, Tai HC. Synthesis of peptides containing 2-oxohistidine residues and their characterization by liquid chromatography-tandem mass spectrometry. J Pept Sci 2015; 21:114-9. [PMID: 25557961 DOI: 10.1002/psc.2735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/09/2014] [Accepted: 12/05/2014] [Indexed: 11/06/2022]
Abstract
Protein oxidation by reactive oxygen species has been associated with aging and neurodegenerative disorders, and histidine is one of the major oxidation targets due to its metal-chelating property and susceptibility to metal-catalyzed oxidation. 2-Oxohistidine, the major product of histidine oxidation, has been recently identified as a stable marker of oxidative damage in biological systems, but its biophysical and biochemical properties are understudied, partly because of difficulties in its chemical synthesis. We developed an efficient method to generate a 2-oxohistidine side chain using metal-catalyzed oxidation, applicable to both monomers and peptides. By optimizing reagent ratios and pH buffering in Cu(2+) /ascorbate/O2 reaction system, we improved the yield more than tenfold compared to reported conditions, which allowed us to obtain homogeneously modified 2-oxohisidine peptides for further studies. Analysis of 2-oxohistidine-containing model peptides by liquid chromatography-tandem mass spectrometry demonstrated increased retention time in reverse-phase chromatography and general stability of 2-oxohistidine under electrospray ionization and collision-induced dissociation. Thus, large-scale analysis of 2-oxohistidine-modified proteome should be feasible using shotgun protein mass spectrometry, and we were able to observe such peptides in proteomics datasets. The feasibility of acquiring purified peptide probes and peptide antigens containing 2-oxohistidine will help advance the study of this non-enzymatic posttranslational modification.
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Affiliation(s)
- Che-Fan Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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49
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Schild F, Kieffer-Jaquinod S, Palencia A, Cobessi D, Sarret G, Zubieta C, Jourdain A, Dumas R, Forge V, Testemale D, Bourguignon J, Hugouvieux V. Biochemical and biophysical characterization of the selenium-binding and reducing site in Arabidopsis thaliana homologue to mammals selenium-binding protein 1. J Biol Chem 2014; 289:31765-31776. [PMID: 25274629 PMCID: PMC4231655 DOI: 10.1074/jbc.m114.571208] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 09/17/2014] [Indexed: 12/19/2022] Open
Abstract
The function of selenium-binding protein 1 (SBP1), present in almost all organisms, has not yet been established. In mammals, SBP1 is known to bind the essential element selenium but the binding site has not been identified. In addition, the SBP family has numerous potential metal-binding sites that may play a role in detoxification pathways in plants. In Arabidopsis thaliana, AtSBP1 over-expression increases tolerance to two toxic compounds for plants, selenium and cadmium, often found as soil pollutants. For a better understanding of AtSBP1 function in detoxification mechanisms, we investigated the chelating properties of the protein toward different ligands with a focus on selenium using biochemical and biophysical techniques. Thermal shift assays together with inductively coupled plasma mass spectrometry revealed that AtSBP1 binds selenium after incubation with selenite (SeO3(2-)) with a ligand to protein molar ratio of 1:1. Isothermal titration calorimetry confirmed the 1:1 stoichiometry and revealed an unexpectedly large value of binding enthalpy suggesting a covalent bond between selenium and AtSBP1. Titration of reduced Cys residues and comparative mass spectrometry on AtSBP1 and the purified selenium-AtSBP1 complex identified Cys(21) and Cys(22) as being responsible for the binding of one selenium. These results were validated by site-directed mutagenesis. Selenium K-edge x-ray absorption near edge spectroscopy performed on the selenium-AtSBP1 complex demonstrated that AtSBP1 reduced SeO3(2-) to form a R-S-Se(II)-S-R-type complex. The capacity of AtSBP1 to bind different metals and selenium is discussed with respect to the potential function of AtSBP1 in detoxification mechanisms and selenium metabolism.
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Affiliation(s)
- Florie Schild
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Sylvie Kieffer-Jaquinod
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Biologie à Grande Echelle, Université Grenoble Alpes, CEA, INSERM, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Andrés Palencia
- European Molecular Biology Laboratory Outstation, 71 avenue des Martyrs, F-38042 Grenoble, France and Unit for Virus Host-Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, Direction des Sciences du Vivant, Institut de Biologie Structurale, 6 rue Jules Horowitz, F-38044 Grenoble, France
| | - Géraldine Sarret
- Université Grenoble Alpes, CNRS & IRD, ISTerre, BP 53, F-38041 Grenoble, France
| | - Chloé Zubieta
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Agnès Jourdain
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Renaud Dumas
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Vincent Forge
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CEA, CNRS, Institut de Recherches en Technologies et Sciences pour le Vivant, 17 rue des Martyrs, F-38000 Grenoble, France, and
| | - Denis Testemale
- Université Grenoble Alpes, CNRS, Institut NEEL, 25 rue des Martyrs, F-38042 Grenoble, France
| | - Jacques Bourguignon
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Véronique Hugouvieux
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359,.
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50
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Degtyar E, Harrington MJ, Politi Y, Fratzl P. Die Bedeutung von Metallionen für die mechanischen Eigenschaften von Biomaterialien auf Proteinbasis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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