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Bian Z, Dong W, Ning Z, Song Y, Hu K. Recovery of terbium by Lysinibacillus sp. DW018 isolated from ionic rare earth tailings based on microbial induced calcium carbonate precipitation. Front Microbiol 2024; 15:1416731. [PMID: 38887713 PMCID: PMC11180810 DOI: 10.3389/fmicb.2024.1416731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Microbial induced calcium carbonate precipitation (MICP) is considered as an environmentally friendly microbial-based technique to remove heavy metals. However, its application in removal and recovery of rare earth from wastewaters remains limited and the process is still less understood. In this study, a urease-producing bacterial strain DW018 was isolated from the ionic rare earth tailings and identified as Lysinibacillus based on 16S rRNA gene sequencing. Its ability and possible mechanism to recover terbium was investigated by using X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and fourier transform infrared spectroscopy (FTIR). The results showed that the urease activity of DW018 could meet the biomineralization requirements for the recovery of Tb3+ from wastewaters. The recovery rate was as high as 98.28% after 10 min of treatment. The optimal conditions for mineralization and recovery were determined as a bacterial concentration of OD600 = 1.0, a temperature range of 35 to 40°C, and a urea concentration of 0.5%. Notably, irrespective of CaCO3 precipitation, the strain DW018 was able to utilize MICP to promote the attachment of Tb3+ to its cell surface. Initially, Tb3+ existed in amorphous form on the bacterial surface; however, upon the addition of a calcium source, Tb3+ was encapsulated in calcite with the growth of CaCO3 at the late stage of the MICP. The recovery effect of the strain DW018 was related to the amino, hydroxyl, carboxyl, and phosphate groups on the cell surface. Overall, the MICP system is promising for the green and efficient recovery of rare earth ions from wastewaters.
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Affiliation(s)
- Zijun Bian
- Jiangxi Provincial Key Laboratory of Environmental Pollution Prevention and Control in Mining and Metallurgy, Ganzhou, China
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Wei Dong
- Jiangxi Provincial Key Laboratory of Environmental Pollution Prevention and Control in Mining and Metallurgy, Ganzhou, China
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, China
- School of Life Sciences, Jiangxi University of Science and Technology, Ganzhou, China
- Yichun Lithium New Energy Industry Research Institute, Jiangxi University of Science and Technology, Yichun, China
| | - Zhoushen Ning
- Jiangxi Provincial Key Laboratory of Environmental Pollution Prevention and Control in Mining and Metallurgy, Ganzhou, China
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Yuexin Song
- Jiangxi Provincial Key Laboratory of Environmental Pollution Prevention and Control in Mining and Metallurgy, Ganzhou, China
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Kaijian Hu
- Jiangxi Provincial Key Laboratory of Environmental Pollution Prevention and Control in Mining and Metallurgy, Ganzhou, China
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, China
- Yichun Lithium New Energy Industry Research Institute, Jiangxi University of Science and Technology, Yichun, China
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Spotts E, Guy N, Lengyel G, Franks J, Maltman C. Chryseobacterium metallicongregator, sp. nov., a bacterium possessing metallophore activity towards rare earth elements. Int J Syst Evol Microbiol 2024; 74. [PMID: 38602172 DOI: 10.1099/ijsem.0.006337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
A polyphasic taxonomic study was carried out on strain ES2T, isolated from sediment of a wetland created to remediate acid drainage from a coal mine. The rod-shaped bacterium formed yellow/orange pigmented colonies and produced the pigment flexirubin. The 16S rRNA gene sequence results assigned the strain to Chryseobacterium, with 98.9 and 98.3 % similarity to Chryseobacterium vietnamense and Chryseobacterium cucumeris, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization values with the closest phylogenetic neighbours of ES2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids of strain ES2T were iso-C15 : 0, iso-C17 : 1 ω9c, iso C17 : 0 3-OH, and iso-C15 : 0 2-OH. The DNA G+C content was 35.5 mol%. The major polar lipid was phosphatidylethanolamine while menaquinone-6 was the only menaquinone found. This bacterium has been previously shown to possess metallophore activity towards rare earth elements, and based on genome sequencing, possesses all required genes for siderophore production/activity, possibly identifying the source of this unique ability. On the basis of the results obtained here, this bacterium is assigned to the genus Chryseobacterium as representing a new species with the name Chryseobacterium metallicongregator sp. nov., type strain ES2T (=NRRL B-65679T=KCTC 102120T).
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Affiliation(s)
- Emily Spotts
- Department of Biology, Slippery Rock University, Slippery Rock, Pennsylvania, 16057, USA
| | - Nathan Guy
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, 16057, USA
| | - George Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, 16057, USA
| | - Jonathan Franks
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, Pennsylvania, 16057, USA
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3
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Skeba S, Snyder M, Maltman C. Metallophore Activity toward the Rare Earth Elements by Bacteria Isolated from Acid Mine Drainage Due to Coal Mining. Microorganisms 2023; 11:2672. [PMID: 38004684 PMCID: PMC10673398 DOI: 10.3390/microorganisms11112672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The field of microbe-metal interactions has been gaining significant attention. While the direct impact of metal oxyanions on bacteria has been investigated, significantly less attention has been placed on the ability of certain microbes to 'collect' such metal ions via secreted proteins. Many bacteria possess low-weight molecules called siderophores, which collect Fe from the environment to be brought back to the cell. However, some appear to have additional roles, including binding other metals, termed 'metallophores'. Microbes can remove/sequester these from their surroundings, but the breadth of those that can be removed is still unknown. Using the Chromeazurol S assay, we identified eight isolates, most belonging to the genus Pseudomonas, possessing siderophore activity, mainly from sites impacted by coal mine drainage, also possessing a metallophore activity toward the rare earth elements that does not appear to be related to ionic radii or previously reported EC50 concentrations for E. coli. We found the strength of metallophore activity towards these elements was as follows: Pr > Sc > Eu > Tm > Tb > Er > Yb > Ce > Lu > Sm > Ho > La > Nd > Dy > Gd > Y. This is the first study to investigate such activity and indicates bacteria may provide a means of removal/recovery of these critical elements.
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Affiliation(s)
| | | | - Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, PA 16057, USA
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4
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Kulasekara DN, Kajjam AB, Praneeth S, Dittrich TM, Allen MJ. Cryptands on a Solid Support for the Separation of Europium from Gadolinium. ACS APPLIED MATERIALS & INTERFACES 2023; 15:42037-42045. [PMID: 37623310 DOI: 10.1021/acsami.3c06975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
With the great demand for europium in green-energy technologies comes the need for innovative methods to isolate the elements. We introduce a solid-liquid extraction method using a 2.2.2-cryptand-modified solid support to separate europium from gadolinium using their differences in electrochemical potential. The method overcomes challenges associated with the separation of those two ions that have similar coordination chemistry in the +3 oxidation state. A competitive adsorption study in the cryptand system between EuII/EuIII and GdIII shows greater affinity for EuII relative to GdIII. After separation from GdIII, Eu was released by oxidizing EuII to EuIII with 99.3% purity. The purity of separated Eu is unaffected by pH between pH 3.0 and 5.5. Overall, we demonstrate that by modifying a solid support with 2.2.2-cryptand, divalent europium can be separated from trivalent gadolinium based on the differences of affinities of 2.2.2-cryptand for the two ions.
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Affiliation(s)
- D Nuwangi Kulasekara
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Aravind B Kajjam
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Sai Praneeth
- Department of Civil and Environmental Engineering, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202, United States
| | - Timothy M Dittrich
- Department of Civil and Environmental Engineering, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202, United States
| | - Matthew J Allen
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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Cui H, Zhang X, Chen J, Qian X, Zhong Y, Ma C, Zhang H, Liu K. The Construction of a Microbial Synthesis System for Rare Earth Enrichment and Material Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303457. [PMID: 37243571 DOI: 10.1002/adma.202303457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Rare earth materials play an irreplaceable role in biomedical and high technology fields. However, typical mining and extraction approaches to rare earth elements (REEs) often lead to severe environmental problems and resource wastage due to the involvement of hazardous chemicals. Although biomining shows elegant alternatives, there are still grand challenges to sustainably isolate and recover REEs in nature because of insufficient metal-extracting microbes and RE-scavenging macromolecular tools. To obtain high-performance rare earth materials directly from rare earth ore, a new generation of biological synthesis strategies needs to be developed for the efficient preparation of REEs. The microbial synthesis system established here has achieved active biomanufacturing of high-purity rare earth products. Further, through employing robust affinity columns bioconjugated with structurally engineered proteins, outstanding separation of Eu/Lu and Dy/La is acquired with the purity of 99.9% (Eu), 97.1% (La), and 92.7% (Dy). More importantly, in situ one-pot synthesis of lanthanide-dependent methanol dehydrogenase is well harnessed and exclusively adsorbs La, Ce, Pr, and Nd in RE tailing for advanced biocatalysis, indicating high value-added application. Therefore, this novel biosynthetic platform provides an insightful roadmap to expand the scope of chassis engineering in terms of biofoundry and to manufacture valuable bioproducts related to REEs.
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Affiliation(s)
- Huijing Cui
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xin Zhang
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jing Chen
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xining Qian
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuewen Zhong
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Chao Ma
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hongjie Zhang
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Kai Liu
- Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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6
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Prejanò M, Toscano M, Marino T. Periodicity of the Affinity of Lanmodulin for Trivalent Lanthanides and Actinides: Structural and Electronic Insights from Quantum Chemical Calculations. Inorg Chem 2023; 62:7461-7470. [PMID: 37128767 DOI: 10.1021/acs.inorgchem.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lanmodulin (LanM) is the first identified macrochelator that has naturally evolved to sequester ions of rare earth elements (REEs) such as Y and all lanthanides, reversibly. This natural protein showed a 106 times better affinity for lanthanide cations than for Ca, which is a naturally abundant and biologically relevant element. Recent experiments have shown that its metal ion binding activity can be further extended to some actinides, like Np, Pu, and Am. For this reason, it was thought that LanM could be adopted for the separation of REE ions and actinides, thus increasing the interest in its potential use for industry-oriented applications. In this work, a systematic study of the affinity of LanM for lanthanides and actinides has been carried out, taking into account all trivalent ions belonging to the 4f (from La to Lu) and 5f (from Ac to Lr) series, starting from their chemistry in solution. On the basis of a recently published nuclear magnetic resonance structure, a model of the LanM-binding site was built and a detailed structural and electronic description of initial aquo- and LanM-metal ion complexes was provided. The obtained binding energies are in agreement with the available experimental data. A possible reason that could explain the origin of the affinity of LanM for these metal ions is also discussed.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Marirosa Toscano
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
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7
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Summers TJ, Sobrinho JA, de Bettencourt-Dias A, Kelly SD, Fulton JL, Cantu DC. Solution Structures of Europium Terpyridyl Complexes with Nitrate and Triflate Counterions in Acetonitrile. Inorg Chem 2023; 62:5207-5218. [PMID: 36940386 DOI: 10.1021/acs.inorgchem.3c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Lanthanide-ligand complexes are key components of technological applications, and their properties depend on their structures in the solution phase, which are challenging to resolve experimentally or computationally. The coordination structure of the Eu3+ ion in different coordination environments in acetonitrile is examined using ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. AIMD simulations are conducted for the solvated Eu3+ ion in acetonitrile, both with or without a terpyridyl ligand, and in the presence of either triflate or nitrate counterions. EXAFS spectra are calculated directly from AIMD simulations and then compared to experimentally measured EXAFS spectra. In acetonitrile solution, both nitrate and triflate anions are shown to coordinate directly to the Eu3+ ion forming either ten- or eight-coordinate solvent complexes where the counterions are binding as bidentate or monodentate structures, respectively. Coordination of a terpyridyl ligand to the Eu3+ ion limits the available binding sites for the solvent and anions. In certain cases, the terpyridyl ligand excludes any solvent binding and limits the number of coordinated anions. The solution structure of the Eu-terpyridyl complex with nitrate counterions is shown to have a similar arrangement of Eu3+ coordinating molecules as the crystal structure. This study illustrates how a combination of AIMD and EXAFS can be used to determine how ligands, solvent, and counterions coordinate with the lanthanide ions in solution.
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Affiliation(s)
- Thomas J Summers
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557-0388, United States
| | - Josiane A Sobrinho
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557-0705, United States
| | | | - Shelly D Kelly
- X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4801, United States
| | - John L Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557-0388, United States
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8
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Jordan RB. Lanthanide Contraction: What is Normal? Inorg Chem 2023; 62:3715-3721. [PMID: 36812146 DOI: 10.1021/acs.inorgchem.2c03674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Renewed interest in lanthanide contraction results from its possible effect on the properties and applications of Ln(III) compounds and the theory related to these issues. To understand this effect, it is important to know what is a normal dependence of the contraction on the number of 4f electrons, n. The normal trend is based on recent values of ionic radii that have a linear dependence on n for coordination numbers (CNs) of 6, 8, and 9. If the normal trend is not followed, then some other interactions in the system are affecting the extent of contraction. However, the suggestion that the variation is curved and fitted by a quadratic function has become popular in recent years. This report examines the Ln(III)-to-ligand atom distances for coordination compounds with CNs of 6-9 and the nitrides and phosphides. Least-squares fits to the linear and quadratic models are applied to all of the bond distances to determine when a quadratic model is justified. The result is that complex systems show a mixture of linear and quadratic dependencies when individual bond distances are considered and that the linear model is most common and representative of the true lanthanide contraction.
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Affiliation(s)
- Robert B Jordan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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9
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Zhang J, Wenzel M, Schnaars K, Hennersdorf F, Lindoy LF, Weigand JJ. Highly Tunable 4-Phosphoryl Pyrazolone Receptors for Selective Rare-Earth Separation. Inorg Chem 2023; 62:3212-3228. [PMID: 36752766 DOI: 10.1021/acs.inorgchem.2c04221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Highly selective rare-earth separation has become increasingly important due to the indispensable role of these elements in various cutting-edge technologies including clean energy. However, the similar physicochemical properties of rare-earth elements (REEs) render their separation very challenging, and the development of new selective receptors for these elements is potentially of very considerable economic and environmental importance. Herein, we report the development of a series of 4-phosphoryl pyrazolone receptors for the selective separation of trivalent lanthanum, europium, and ytterbium as the representatives of light, middle, and heavy REEs, respectively. X-ray crystallography studies were employed to obtain solid-state structures across 11 of the resulting complexes, allowing comparative structure-function relationships to be probed, including the effect of lanthanide contraction that occurs along the series from lanthanum to europium to ytterbium and which potentially provides a basis for REE ion separation. In addition, the influence of ligand structure and lipophilicity on lanthanide binding and selectivity was systematically investigated via n-octanol/water distribution and liquid-liquid extraction (LLE) studies. Corresponding stoichiometry relationships between solid and solution states were well established using slope analyses. The results provide new insights into some fundamental lanthanide coordination chemistry from a separation perspective and establish 4-phosphoryl pyrazolone derivatives as potential practical extraction reagents for the selective separation of REEs in the future.
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Affiliation(s)
- Jianfeng Zhang
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, Dresden 01062, Germany
| | - Marco Wenzel
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, Dresden 01062, Germany
| | - Kathleen Schnaars
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, Dresden 01062, Germany
| | - Felix Hennersdorf
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, Dresden 01062, Germany
| | - Leonard F Lindoy
- School of Chemistry, F11, University of Sydney, New South Wales 2006, Sydney, Australia
| | - Jan J Weigand
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, Dresden 01062, Germany.,Department of Chemistry and Polymer Science, Stellenbosch University, Stellenbosch 7600, South Africa
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Daumann LJ, Pol A, Op den Camp HJM, Martinez-Gomez NC. A perspective on the role of lanthanides in biology: Discovery, open questions and possible applications. Adv Microb Physiol 2022; 81:1-24. [PMID: 36167440 DOI: 10.1016/bs.ampbs.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Because of their use in high technologies like computers, smartphones and renewable energy applications, lanthanides (belonging to the group of rare earth elements) are essential for our daily lives. A range of applications in medicine and biochemical research made use of their photo-physical properties. The discovery of a biological role for lanthanides has boosted research in this new field. Several methanotrophs and methylotrophs are strictly dependent on the presence of lanthanides in the growth medium while others show a regulatory response. After the first demonstration of a lanthanide in the active site of the XoxF-type pyrroloquinoline quinone methanol dehydrogenases, follow-up studies showed the same for other pyrroloquinoline quinone-containing enzymes. In addition, research focused on the effect of lanthanides on regulation of gene expression and uptake mechanism into bacterial cells. This review briefly describes the discovery of the role of lanthanides in biology and focuses on open questions in biological lanthanide research and possible application of lanthanide-containing bacteria and enzymes in recovery of these special elements.
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Affiliation(s)
- Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Arjan Pol
- Department of Microbiology, RIBES, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, RIBES, Radboud University, Nijmegen, The Netherlands.
| | - N Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States
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Guo HB, Perminov A, Bekele S, Kedziora G, Farajollahi S, Varaljay V, Hinkle K, Molinero V, Meister K, Hung C, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 models indicate that protein sequence determines both structure and dynamics. Sci Rep 2022; 12:10696. [PMID: 35739160 PMCID: PMC9226352 DOI: 10.1038/s41598-022-14382-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.
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Affiliation(s)
- Hao-Bo Guo
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Alexander Perminov
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- Computer Science Department, Miami University, Oxford, OH, USA
| | - Selemon Bekele
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Gary Kedziora
- General Dynamics Information Technology, Inc., Wright-Patterson Air Force Base, 45433, OH, USA
| | - Sanaz Farajollahi
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Vanessa Varaljay
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Kevin Hinkle
- Department of Chemical and Materials Engineering, Dayton University, Dayton, OH, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, UT, USA
| | - Konrad Meister
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Chia Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Patrick Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
| | - Rajiv Berry
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
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