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Bieber P, Borduas-Dedekind N. High-speed cryo-microscopy reveals that ice-nucleating proteins of Pseudomonas syringae trigger freezing at hydrophobic interfaces. SCIENCE ADVANCES 2024; 10:eadn6606. [PMID: 38959312 PMCID: PMC11221516 DOI: 10.1126/sciadv.adn6606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/22/2024] [Indexed: 07/05/2024]
Abstract
Ice-nucleating proteins (INpro) trigger the freezing of supercooled water droplets relevant to atmospheric, biological, and technological applications. The high ice nucleation activity of INpro isolated from the bacteria Pseudomonas syringae could be linked to the aggregation of proteins at the bacterial membrane or at the air-water interface (AWI) of droplets. Here, we imaged freezing onsets, providing direct evidence of these proposed mechanisms. High-speed cryo-microscopy identified the onset location of freezing in droplets between two protein-repellent glass slides. INpro from sterilized P. syringae (Snomax) statistically favored nucleation at the AWI of the droplets. Removing cellular fragments by filtration or adding surfactants increased the frequency of nucleation events at the AWI. On the other hand, cultivated intact bacteria cells or lipid-free droplets nucleated ice without an affinity to the AWI. Overall, we provide visual evidence that INpro from P. syringae trigger freezing at hydrophobic interfaces, such as the AWI or the bacterial membrane, with important mechanistic implications for applications of INpro.
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2
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Uko MP, Umana SI, Iwatt IJ, Udoekong NS, Mgbechidinma CL, Adie FU, Akan OD. Microbial ice-binding structures: A review of their applications. Int J Biol Macromol 2024; 275:133670. [PMID: 38971293 DOI: 10.1016/j.ijbiomac.2024.133670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/02/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
Microorganisms' ice-binding structures (IBS) are macromolecules with potential commercial value in agriculture, food technology, material technology, cryobiology, and medicine. Microbial ice-structuring or microbial ice-binding particles, with their multi-applications, are simple to use, effective in low amounts, non-toxic, and environmentally friendly. Due to their source and composition diversities, microbial ice-binding structures are gaining attention because they are useable in various conditions. Some microorganisms also produce structures with dual ice-nucleating and anti-freezing properties. Structures that promote ice formation (ice nucleating particles- INPs) act as ice nuclei, lowering the energy barrier between supercooled liquid and ice, causing ice crystals to form. In contrast, anti-freeze particles (AFPs) prevent ice formation and recrystallization through several mechanisms, including disturbing the formation of string hydrogen bonds amongst water molecules, melting already formed ice crystals, and preventing crystal formation by binding to specific sites. Knowledge of the type and function of microbial ice-binding structures lends fundamental insight for possible scaling the production of cheap, functional, and advanced microbial structure-inspired mimics and by-products. This review focuses on microbial ice-binding structures and their potential uses in the food, medicinal, environmental, and agricultural sectors.
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Affiliation(s)
- Mfoniso Peter Uko
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria
| | - Senyene Idorenyin Umana
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria; Department of Microbiology, Faculty of Michael Okpara of Agriculture, Umudike, Nigeria
| | - Ifiok Joseph Iwatt
- Center for Wetlands and Wastes Management Studies, Faculty of Agriculture, University of Uyo, Uyo, Nigeria
| | | | - Chiamaka Linda Mgbechidinma
- School of Life Sciences, Centre for Cell and Development Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Microbiology, University of Ibadan, Ibadan 200243, Nigeria
| | - Francisca Upekiema Adie
- Department of Microbiology, Faculty of Biological Sciences, Cross River State University of Technology, Calabar, Nigeria
| | - Otobong Donald Akan
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria; College of Food Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, China.
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3
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Lu H, Macht M, Rosenberg R, Wiedenbeck E, Lukas M, Qi D, Maltseva D, Zahn D, Cölfen H, Bonn M. Organic Nucleation: Water Rearrangement Reveals the Pathway of Ibuprofen. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307858. [PMID: 38269485 DOI: 10.1002/smll.202307858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/31/2023] [Indexed: 01/26/2024]
Abstract
The organic nucleation of the pharmaceutical ibuprofen is investigated, as triggered by the protonation of ibuprofen sodium salt at elevated pH. The growth and aggregation of nanoscale solution species by Analytical Ultracentrifugation and Molecular Dynamics (MD) simulations is tracked. Both approaches reveal solvated molecules, oligomers, and prenucleation clusters, their size as well as their hydration at different reaction stages. By combining surface-specific vibrational spectroscopy and MD simulations, water interacting with ibuprofen at the air-water interface during nucleation is probed. The results show the structure of water changes upon ibuprofen protonation in response to the charge neutralization. Remarkably, the water structure continues to evolve despite the saturation of protonated ibuprofen at the hydrophobic interface. This further water rearrangement is associated with the formation of larger aggregates of ibuprofen molecules at a late prenucleation stage. The nucleation of ibuprofen involves ibuprofen protonation and their hydrophobic assembly. The results highlight that these processes are accompanied by substantial water reorganization. The critical role of water is possibly relevant for organic nucleation in aqueous environments in general.
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Affiliation(s)
- Hao Lu
- Department of Materials and Textile Engineering, Nanotechnology Research Institute, Jiaxing University, Jiaxing, Zhejiang Province, 314001, P. R. China
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Moritz Macht
- Lehrstuhl für Theoretische Chemie/Computer Chemie Centrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany
| | - Rose Rosenberg
- Physical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Eduard Wiedenbeck
- Physical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Max Lukas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Daizong Qi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Daria Maltseva
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Dirk Zahn
- Lehrstuhl für Theoretische Chemie/Computer Chemie Centrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany
| | - Helmut Cölfen
- Physical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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4
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Gunwant V, Gahtori P, Varanasi SR, Pandey R. Protein-Mediated Changes in Membrane Fluidity and Ordering: Insights into the Molecular Mechanism and Implications for Cellular Function. J Phys Chem Lett 2024; 15:4408-4415. [PMID: 38625684 DOI: 10.1021/acs.jpclett.3c03627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Probing protein-membrane interactions is vital for understanding biological functionality for various applications such as drug development, targeted drug delivery, and creation of functional biomaterials for medical and industrial purposes. In this study, we have investigated interaction of Human Serum Albumin (HSA) with two different lipids, dipalmitoylphosphatidylglycerol (dDPPG) and dipalmitoylphosphatidylcholine (dDPPC), using Vibrational Sum Frequency Generation spectroscopy at different membrane fluidity values. In the liquid-expanded (LE) state of the lipid, HSA (at pH 3.5) deeply intercalated lipid chains through a combination of electrostatic and hydrophobic interactions, which resulted in more ordering of the lipid chains. However, in the liquid-condensed (LC) state, protein intercalation is decreased due to tighter lipid packing. Moreover, our findings revealed distinct differences in HSA's interaction with dDPPG and dDPPC lipids. The interaction with dDPPC remained relatively weak compared to dDPPG. These results shed light on the significance of protein mediated changes in lipid characteristics, which hold considerable implications for understanding membrane protein behavior, lipid-mediated cellular processes, and lipid-based biomaterial design.
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Affiliation(s)
- Vineet Gunwant
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Preeti Gahtori
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Srinivasa Rao Varanasi
- Department of Physics, Sultan Qaboos University, P.O. Box 36, Al-Khoud 123, Muscat, Oman
| | - Ravindra Pandey
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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5
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Zhu S, Yang R, Li HJW, Huang S, Wang H, Liu Y, Li H, Zhai T. Reconstructing Hydrogen-Bond Network for Efficient Acidic Oxygen Evolution. Angew Chem Int Ed Engl 2024; 63:e202319462. [PMID: 38286750 DOI: 10.1002/anie.202319462] [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: 12/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 01/31/2024]
Abstract
Developing highly active oxygen evolution reaction (OER) catalysts in acidic conditions is a pressing demand for proton-exchange membrane water electrolysis. Manipulating proton character at the electrified interface, as the crux of all proton-coupled electrochemical reactions, is highly desirable but elusive. Herein we present a promising protocol, which reconstructs a connected hydrogen-bond network between the catalyst-electrolyte interface by coupling hydrophilic units to boost acidic OER activity. Modelling on N-doped-carbon-layer clothed Mn-doped-Co3O4 (Mn-Co3O4@CN), we unravel that the hydrogen-bond interaction between CN units and H2O molecule not only drags the free water to enrich the surface of Mn-Co3O4 but also serves as a channel to promote the dehydrogenation process. Meanwhile, the modulated local charge of the Co sites from CN units/Mn dopant lowers the OER barrier. Therefore, Mn-Co3O4@CN surpasses RuO2 at high current density (100 mA cm-2 @ ~538 mV).
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Affiliation(s)
- Shicheng Zhu
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Ruoou Yang
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Huang Jing Wei Li
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Sirui Huang
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Haozhi Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, and School of Materials Science and Engineering, Hainan University, Haikou, Hainan, 570228, P. R. China
| | - Youwen Liu
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Huiqiao Li
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Tianyou Zhai
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
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6
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Soni A, Patey GN. Using machine learning with atomistic surface and local water features to predict heterogeneous ice nucleation. J Chem Phys 2024; 160:124501. [PMID: 38530008 DOI: 10.1063/5.0177706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Heterogeneous ice nucleation (HIN) has applications in climate science, nanotechnology, and cryopreservation. Ice nucleation on the earth's surface or in the atmosphere usually occurs heterogeneously involving foreign substrates, known as ice nucleating particles (INPs). Experiments identify good INPs but lack sufficient microscopic resolution to answer the basic question: What makes a good INP? We employ molecular dynamics (MD) simulations in combination with machine learning (ML) to address this question. Often, the large amount of computational cost required to cross the nucleation barrier and observe HIN in MD simulations is a practical limitation. We use information obtained from short MD simulations of atomistic surface and water models to predict the likelihood of HIN. We consider 153 atomistic substrates with some surfaces differing in elemental composition and others only in terms of lattice parameters, surface morphology, or surface charges. A range of water features near the surface (local) are extracted from short MD simulations over a time interval (≤300 ns) where ice nucleation has not initiated. Three ML classification models, Random Forest (RF), support vector machine, and Gaussian process classification are considered, and the accuracies achieved by all three approaches lie within their statistical uncertainties. Including local water features is essential for accurate prediction. The accuracy of our best RF classification model obtained including both surface and local water features is 0.89 ± 0.05. A similar accuracy can be achieved including only local water features, suggesting that the important surface properties are largely captured by the local water features. Some important features identified by ML analysis are local icelike structures, water density and polarization profiles perpendicular to the surface, and the two-dimensional lattice match to ice. We expect that this work, with its strong focus on realistic surface models, will serve as a guide to the identification or design of substrates that can promote or discourage ice nucleation.
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Affiliation(s)
- Abhishek Soni
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - G N Patey
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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7
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Alsante A, Thornton DCO, Brooks SD. Effect of Aggregation and Molecular Size on the Ice Nucleation Efficiency of Proteins. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4594-4605. [PMID: 38408303 PMCID: PMC10938890 DOI: 10.1021/acs.est.3c06835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/28/2024]
Abstract
Aerosol acts as ice-nucleating particles (INPs) by catalyzing the formation of ice crystals in clouds at temperatures above the homogeneous nucleation threshold (-38 °C). In this study, we show that the immersion mode ice nucleation efficiency of the environmentally relevant protein, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), occurs at temperatures between -6.8 and -31.6 °C. Further, we suggest that this range is controlled by the RuBisCO concentration and protein aggregation. The warmest median nucleation temperature (-7.9 ± 0.8 °C) was associated with the highest concentration of RuBisCO (2 × 10-1 mg mL-1) and large aggregates with a hydrodynamic diameter of ∼103 nm. We investigated four additional chemically and structurally diverse proteins, plus the tripeptide glutathione, and found that each of them was a less effective INP than RuBisCO. Ice nucleation efficiency of the proteins was independent of the size (molecular weight) for the five proteins investigated in this study. In contrast to previous work, increasing the concentration and degree of aggregation did not universally increase ice nucleation efficiency. RuBisCO was the exception to this generalization, although the underlying molecular mechanism determining why aggregated RuBisCO is such an effective INP remains elusive.
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Affiliation(s)
- Alyssa
N. Alsante
- Department
of Oceanography, Texas A&M University, College Station, Texas 77843, United States
| | - Daniel C. O. Thornton
- Department
of Oceanography, Texas A&M University, College Station, Texas 77843, United States
| | - Sarah D. Brooks
- Department
of Atmospheric Sciences, Texas A&M University, College Station, Texas 77843, United States
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8
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Sung W, Inoue KI, Nihonyanagi S, Tahara T. Unified picture of vibrational relaxation of OH stretch at the air/water interface. Nat Commun 2024; 15:1258. [PMID: 38341439 DOI: 10.1038/s41467-024-45388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The elucidation of the energy dissipation process is crucial for understanding various phenomena occurring in nature. Yet, the vibrational relaxation and its timescale at the water interface, where the hydrogen-bonding network is truncated, are not well understood and are still under debate. In the present study, we focus on the OH stretch of interfacial water at the air/water interface and investigate its vibrational relaxation by femtosecond time-resolved, heterodyne-detected vibrational sum-frequency generation (TR-HD-VSFG) spectroscopy. The temporal change of the vibrationally excited hydrogen-bonded (HB) OH stretch band (ν=1→2 transition) is measured, enabling us to determine reliable vibrational relaxation (T1) time. The T1 times obtained with direct excitations of HB OH stretch are 0.2-0.4 ps, which are similar to the T1 time in bulk water and do not noticeably change with the excitation frequency. It suggests that vibrational relaxation of the interfacial HB OH proceeds predominantly with the intramolecular relaxation mechanism as in the case of bulk water. The delayed rise and following decay of the excited-state HB OH band are observed with excitation of free OH stretch, indicating conversion from excited free OH to excited HB OH (~0.9 ps) followed by relaxation to low-frequency vibrations (~0.3 ps). This study provides a complete set of the T1 time of the interfacial OH stretch and presents a unified picture of its vibrational relaxation at the air/water interface.
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Affiliation(s)
- Woongmo Sung
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Ken-Ichi Inoue
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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9
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Qi D, Lukić MJ, Lu H, Gebauer D, Bonn M. Role of Water during the Early Stages of Iron Oxyhydroxide Formation by a Bacterial Iron Nucleator. J Phys Chem Lett 2024; 15:1048-1055. [PMID: 38253017 DOI: 10.1021/acs.jpclett.3c03327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Understanding the nucleation of iron oxides and the underlying hydrolysis of aqueous iron species is still challenging, and molecular-level insights into the orchestrated response of water, especially at the hydrolysis interface, are lacking. We follow iron(III) hydrolysis in the presence of a synthetic bacterial iron nucleator, which is a magnetosome membrane specific peptide, by using a constant pH titration technique. Three distinct hydrolysis regimes were identified. Interface-selective sum frequency generation (SFG) spectroscopy was used to probe the interfacial reaction and water in direct contact with the peptide. SFG data reveal that iron(III) species react quickly with interfacial peptides while continuously enhancing water alignment into the later stages of hydrolysis. The gradually aligning water molecules are associated with initially promoted (regimes I and II) and later suppressed (regime III) hydrolysis after the saturation of water alignment has occurred until regime II. These interfacial insights are crucial for understanding the early stage of iron oxide biomineralization.
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Affiliation(s)
- Daizong Qi
- Department of Materials and Textile Engineering, Nanotechnology Research Institute, Jiaxing University, Building No. 7, Jiaxing Intelligent Industry & Innovation Park, Jiaxing, Zhejiang 314001, P. R. China
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Miodrag J Lukić
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstrasse 9, 30167 Hannover, Germany
| | - Hao Lu
- Department of Materials and Textile Engineering, Nanotechnology Research Institute, Jiaxing University, Building No. 7, Jiaxing Intelligent Industry & Innovation Park, Jiaxing, Zhejiang 314001, P. R. China
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstrasse 9, 30167 Hannover, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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10
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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [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] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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11
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Hudait A. Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins. Methods Mol Biol 2024; 2730:185-202. [PMID: 37943459 DOI: 10.1007/978-1-0716-3503-2_13] [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: 11/10/2023]
Abstract
Ice-binding proteins (IBPs) are a diverse class of proteins that are essential for the survival of organisms in cold conditions. IBPs are diverse in their function and can prevent or promote ice growth and selectively bind to specific crystallographic planes of the growing ice lattice. Moreover, IBPs are widely utilized to modulate ice crystal growth and recrystallization in the food industry and as cryoprotectants to preserve biological matter. A key unresolved aspect of the mode of action is how the ice-binding sites of these proteins distinguish between ice and water and interact with multiple crystal facets of the ice. The use of molecular dynamics (MD) simulation allows us to thoroughly investigate the binding mechanism and energetics of ice-binding proteins, to complement and expand on the mechanistic understandings gained from experiments. In this chapter, we describe a series of molecular dynamics simulation methodologies to investigate the mechanism of action of ice-binding proteins. Specifically, we provide detailed instructions to set up MD simulations to study the binding and interaction of ice-binding proteins using atomistic and coarse-grained simulations.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL, USA.
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12
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Lei Z, Chen B, Brooks SD. Effect of Acidity on Ice Nucleation by Inorganic-Organic Mixed Droplets. ACS EARTH & SPACE CHEMISTRY 2023; 7:2562-2573. [PMID: 38148991 PMCID: PMC10749479 DOI: 10.1021/acsearthspacechem.3c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Aerosol acidity significantly influences heterogeneous chemical reactions and human health. Additionally, acidity may play a role in cloud formation by modifying the ice nucleation properties of inorganic and organic aerosols. In this work, we combined our well-established ice nucleation technique with Raman microspectroscopy to study ice nucleation in representative inorganic and organic aerosols across a range of pH conditions (pH -0.1 to 5.5). Homogeneous nucleation was observed in systems containing ammonium sulfate, sulfuric acid, and sucrose. In contrast, droplets containing ammonium sulfate mixed with diethyl sebacate, poly(ethylene glycol) 400, and 1,2,6-hexanetriol were found to undergo liquid-liquid phase separation, exhibiting core-shell morphologies with observed initiation of heterogeneous freezing in the cores. Our experimental findings demonstrate that an increased acidity reduces the ice nucleation ability of droplets. Changes in the ratio of bisulfate to sulfate coincided with shifts in ice nucleation temperatures, suggesting that the presence of bisulfate may decrease the ice nucleation efficiency. We also report on how the morphology and viscosity impact ice nucleation properties. This study aims to enhance our fundamental understanding of acidity's effect on ice nucleation ability, providing context for the role of acidity in atmospheric ice cloud formation.
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Affiliation(s)
- Ziying Lei
- Department of Atmospheric
Science, Texas A&M University, College Station, Texas 77843, United States
| | - Bo Chen
- Department of Atmospheric
Science, Texas A&M University, College Station, Texas 77843, United States
| | - Sarah D. Brooks
- Department of Atmospheric
Science, Texas A&M University, College Station, Texas 77843, United States
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13
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Gahtori P, Gunwant V, Pandey R. How Does pH Affect the Adsorption of Human Serum Protein in the Presence of Hydrophobic and Hydrophilic Nanoparticles at Air-Water and Lipid-Water Interfaces? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15487-15498. [PMID: 37878019 DOI: 10.1021/acs.langmuir.3c01755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
This study investigates interaction between hydrophilic (11-mercaptoundecanoic acid (MUA)) and hydrophobic (1-undecanethiol (UDT)) gold nanoparticles (GNPs) with human serum albumin (HSA) protein on air-water and lipid-water interfaces at pH 3 and 7. Vibrational sum frequency generation (VSFG) spectroscopy is used to analyze changes in the intensity of interfacial water molecules and the C-H group of the protein. At the air-water interface, the hydrophobic interaction between the HSA protein and hydrophobic GNPs at pH 3 leads to their accumulation at the interface, resulting in an increased C-H intensity of the protein with a slight decrease in water intensity. Whereas, at pH 7, where the negative charge of the protein results in the reduced surface activity of the HSA compared to pH 3, the interaction between alkyl chain of the hydrophobic GNPs and alkyl group of the protein results in the adsorption of the protein-capped GNPs at the interface. This leads to an increased intensity of the C-H group of protein and water molecules. However, negatively charged hydrophilic GNPs do not induce significant changes in the interfacial water structure or the C-H group of the protein due to the electrostatic force of repulsion with the negatively charged HSA at pH 7. In contrast, at the lipid-water interface, both hydrophobic and hydrophilic GNPs interact with HSA protein, causing disordering of interfacial water molecules at pH 3 and ordering at pH 7. Interestingly, similar behavior of the protein with both types of GNPs results in comparable ordering/disordering at the interface depending on the pH of solution. Furthermore, the VSFG results obtained with the deuterated lipid suggest that changes in ordering and disorder occur due to increased protein adsorption in the presence of GNPs, causing alterations in the membrane structure. These findings give a better understanding of the mechanisms that govern protein-nanoparticle interaction and their consequential effects on the structure, function, and behavior of molecules at the biological membrane interface, which is crucial for developing safe and effective nanoparticle-based therapeutics.
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Affiliation(s)
- Preeti Gahtori
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Vineet Gunwant
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ravindra Pandey
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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14
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Zihan S, Lu L, Tao W, Bolin Z, Hongfei Z. Starch nanoparticles as a new ice crystal nucleator in Lactobacillus bulgaricus CICC 6097 cryoprotection. Int J Biol Macromol 2023; 251:126395. [PMID: 37595719 DOI: 10.1016/j.ijbiomac.2023.126395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/22/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
This work aimed at studying the cryoprotective effect of starch nanoparticles (SNPs) as ice nucleators on Lactobacillus bulgaricus CICC 6097 and exploring the protective mechanism. SNPs with a diameter of 363 nm were obtained, which possessed special properties to enhance ice nucleation and blunt ice crystals edges, and can be wrapped around the surface of bacteria form a protective barrier, thus maintaining the integrity of cell membranes and improving the survivability of L. bulgaricus CICC 6097 from 36.09% to 75.56%. However, SNCs solution formed ice crystals with obvious spikes during freezing, which was harmful to bacteria survival. Therefore, SNPs addition is a possible strategy for increasing viable cell counts during freezing. To the best of our knowledge, this report is the first to demonstrate the cryoprotective effect of ice nucleator on lactic acid bacteria.
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Affiliation(s)
- Sun Zihan
- College of Biological Science & Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing 100083, China
| | - Liu Lu
- College of Biological Science & Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing 100083, China
| | - Wang Tao
- College of Biological Science & Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing 100083, China
| | - Zhang Bolin
- College of Biological Science & Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing 100083, China
| | - Zhao Hongfei
- College of Biological Science & Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing 100083, China.
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15
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Jahed KR, Saini AK, Sherif SM. Coping with the cold: unveiling cryoprotectants, molecular signaling pathways, and strategies for cold stress resilience. FRONTIERS IN PLANT SCIENCE 2023; 14:1246093. [PMID: 37649996 PMCID: PMC10465183 DOI: 10.3389/fpls.2023.1246093] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Low temperature stress significantly threatens crop productivity and economic sustainability. Plants counter this by deploying advanced molecular mechanisms to perceive and respond to cold stress. Transmembrane proteins initiate these responses, triggering a series of events involving secondary messengers such as calcium ions (Ca2+), reactive oxygen species (ROS), and inositol phosphates. Of these, calcium signaling is paramount, activating downstream phosphorylation cascades and the transcription of cold-responsive genes, including cold-regulated (COR) genes. This review focuses on how plants manage freeze-induced damage through dual strategies: cold tolerance and cold avoidance. Tolerance mechanisms involve acclimatization to decreasing temperatures, fostering gradual accumulation of cold resistance. In contrast, avoidance mechanisms rely on cryoprotectant molecules like potassium ions (K+), proline, glycerol, and antifreeze proteins (AFPs). Cryoprotectants modulate intracellular solute concentration, lower the freezing point, inhibit ice formation, and preserve plasma membrane fluidity. Additionally, these molecules demonstrate antioxidant activity, scavenging ROS, preventing protein denaturation, and subsequently mitigating cellular damage. By forming extensive hydrogen bonds with water molecules, cryoprotectants also limit intercellular water movement, minimizing extracellular ice crystal formation, and cell dehydration. The deployment of cryoprotectants is a key adaptive strategy that bolsters plant resilience to cold stress and promotes survival in freezing environments. However, the specific physiological and molecular mechanisms underlying these protective effects remain insufficiently understood. Therefore, this review underscores the need for further research to elucidate these mechanisms and assess their potential impact on crop productivity and sustainability, contributing to the progressive discourse in plant biology and environmental science.
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Affiliation(s)
| | | | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA, United States
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16
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Aich R, Pal P, Chakraborty S, Jana B. Preferential Ordering and Organization of Hydration Water Favor Nucleation of Ice by Ice-Nucleating Proteins over Antifreeze Proteins. J Phys Chem B 2023; 127:6038-6048. [PMID: 37395194 DOI: 10.1021/acs.jpcb.3c01641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Bacteria containing ice-nucleating proteins (INPs) evolved in nature to nucleate ice at the high sub-zero ambiance. The ability of the INPs to induce order in the hydration layer and their aggregation propensity appear to be key factors of their ice nucleation abilities. However, the mechanism of the process of ice nucleation by INPs is yet to be understood clearly. Here, we have performed all-atom molecular dynamics simulations and analyzed the structure and dynamics of the hydration layer around the proposed ice-nucleating surface of a model INP. Results are compared with the hydration of a topologically similar non-ice-binding protein (non-IBP) and another ice-growth inhibitory antifreeze protein (sbwAFP). We observed that the hydration structure around the ice-nucleating surface of INP is highly ordered and the dynamics of the hydration water are slower, compared to the non-IBP. Even the ordering of the hydration layer is more evident around the ice-binding surface of INP, compared to the antifreeze protein sbwAFP. Particularly with increasing repeat units of INP, we observe an increased population of ice-like water. Interestingly, the distances between the hydroxyl groups of the threonine ladder and its associated channel water of the ice-binding surface (IBS) of INP in the X and Y direction mimic the oxygen atom distances of the basal plane of hexagonal ice. However, the structural synergies between the hydroxyl group distances of the threonine ladder and its associated channel water of the IBS of sbwAFP and oxygen atom distances of the basal plane are less evident. This difference makes the IBS of the INP a better template for ice nucleation than AFP, although both of them bind to the ice surface efficiently.
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Affiliation(s)
- Rahul Aich
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prasun Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institution of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 5000046, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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17
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Lindow S. History of Discovery and Environmental Role of Ice Nucleating Bacteria. PHYTOPATHOLOGY 2023; 113:605-615. [PMID: 36122194 DOI: 10.1094/phyto-07-22-0256-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The phenomenon of biological ice nucleation that is exhibited by a variety of bacteria is a fascinating phenotype, which has been shown to incite frost damage to frost-sensitive plants and has been proposed to contribute to atmospheric processes that affect the water cycle and earth's radiation balance. This review explores the several possible drivers for the evolutionary origin of the ice nucleation phenotype. These bacteria and the gene required for this phenotype have also been exploited in processes as diverse as reporter gene assays to assess environmentally responsive gene expression in various plant pathogenic and environmental bacteria and in the detection of foodborne human pathogens when coupled with host-specific bacteriophage, whereas ice nucleating bacteria themselves have been exploited in the production of artificial snow for recreation and oil exploration and in the process of freezing of various food products. This review also examines the historical development of our understanding of ice nucleating bacteria, details of the genetic determinants of ice nucleation, and features of the aggregates of membrane-bound ice nucleation protein necessary for catalyzing ice. Lastly, this review also explores the role of these bacteria in limiting the supercooling ability of plants and the strategies and limitations of avoiding plant frost damage by managing these bacterial populations by bactericides, antagonistic bacteria, or cultural control strategies.
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Affiliation(s)
- Steven Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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18
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Fuentes OP, Osma JF. Life Cycle Assessment of Functionalized Bionanocompounds with Ice Nucleation Protein for Freezing Applications. Polymers (Basel) 2023; 15:polym15061457. [PMID: 36987237 PMCID: PMC10058881 DOI: 10.3390/polym15061457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
The objective of this study was to assess the effectiveness of functionalized bionanocompounds with ice nucleation protein (INP) as a novel approach for freezing applications in terms of how much energy is used during each step of freezing when water bionanocompound solutions were compared with pure water. According to the results of the manufacturing analysis, water required 28 times less energy than the silica + INA bionanocompound and 14 times less than the magnetite + INA bionanocompound. These findings showed that water used the least energy during the manufacturing process. In order to determine the associated environmental implications, an analysis of the operating stage was also conducted, taking the defrosting time of each bionanocompound during a 4 h work cycle into account. Our results showed that bionanocompounds may substantially reduce the environmental effects by achieving a 91% reduction in the impact after their use during all four work cycles in the operation stage. Additionally, given the energy and raw materials needed in this process, this improvement was more significant than at the manufacturing stage. The results from both stages indicated that, when compared with water, the magnetite + INA bionanocompound and the silica + INA bionanocompound would save an estimated 7% and 47% of total energy, respectively. The study’s findings also demonstrated the great potential for using bionanocompounds in freezing applications to reduce the effects on the environment and human health.
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Affiliation(s)
- Olga P. Fuentes
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Cra. 1E No. 19a-40, Bogota 111711, Colombia
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Cra. 1E No. 19a-40, Bogota 111711, Colombia
- Department of Biomedical Engineering, Universidad de los Andes, Cra. 1E No. 19a-40, Bogota 111711, Colombia
- Correspondence: ; Tel.: +57-601-3394-949
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19
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Guo W, Lu T, Crisci R, Nagao S, Wei T, Chen Z. Determination of protein conformation and orientation at buried solid/liquid interfaces. Chem Sci 2023; 14:2999-3009. [PMID: 36937592 PMCID: PMC10016606 DOI: 10.1039/d2sc06958j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Protein structures at solid/liquid interfaces mediate interfacial protein functions, which are important for many applications. It is difficult to probe interfacial protein structures at buried solid/liquid interfaces in situ at the molecular level. Here, a systematic methodology to determine protein molecular structures (orientation and conformation) at buried solid/liquid interfaces in situ was successfully developed with a combined approach using a nonlinear optical spectroscopic technique - sum frequency generation (SFG) vibrational spectroscopy, isotope labeling, spectra calculation, and computer simulation. With this approach, molecular structures of protein GB1 and its mutant (with two amino acids mutated) were investigated at the polymer/solution interface. Markedly different orientations and similar (but not identical) conformations of the wild-type protein GB1 and its mutant at the interface were detected, due to the varied molecular interfacial interactions. This systematic strategy is general and can be widely used to elucidate protein structures at buried interfaces in situ.
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Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Tieyi Lu
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Ralph Crisci
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Satoshi Nagao
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Ako-gun Kamigouri-cho Hyogo 678-1297 Japan
| | - Tao Wei
- Department of Chemical Engineering, Howard University 2366 Sixth Street NW Washington 20059 DC USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
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20
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Chen X, Wu J, Yang F, Zhou M, Wang R, Huang J, Rong Y, Liu J, Wang S. New insight into the mechanism by which antifreeze peptides regulate the physiological function of Streptococcus thermophilus subjected to freezing stress. J Adv Res 2023; 45:127-140. [PMID: 35599106 PMCID: PMC10006524 DOI: 10.1016/j.jare.2022.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/14/2022] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Antifreeze peptides regulate the physiological functions of frozen cells and even their apoptosis; however, the mechanisms by which antifreeze peptides regulate these processes remain unclear, although the interactions between cell membranes and ice are well known to be important in this process. OBJECTIVES Our study aims to investigate how antifreeze peptides regulate cell physiological functions during the freezing process. METHODS We investigated the cryoprotective effect of rsfAFP on the physiological functions of S. thermophilus under freezing stress by measuring cellular metabolism activity, intracellular enzyme activity, cell membrane characterization, and cell apoptosis. The mechanism by which rsfAFP impacts S. thermophilus physiological functions under freezing stress was investigated using multispectral techniques and cryo-TEM. RESULTS We show that a recombinant antifreeze peptide (rsfAFP) interacts with the extracellular capsular polysaccharides and peptidoglycan of Streptococcus thermophilus and ice to cover the outer layer of the membrane, forming a dense protective layer that regulates the molecular structure of extracellular ice crystals, which results in reduced extracellular membrane damage, depressed apoptosis and increased intracellular metabolic activity. This interaction mechanism was indicated by the fact that S. thermophilus better maintained its permeability barrier, membrane fluidity, membrane structural integrity, and cytoplasmic membrane potential during freezing stress with rsfAFP treatment. CONCLUSION These results provide new insights into the mechanism by which rsfAFP regulates frozen cellphysiological functionsand apoptosis under freezing stress.
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Affiliation(s)
- Xu Chen
- School of Mechanical Science & Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fujia Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Mi Zhou
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruibin Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing of Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
| | - Yuzhi Rong
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jianhua Liu
- International Faculty of Applied Technology, Yibin University, Yibin, Sichuan 644000, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China.
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21
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Zheng RH, Wei WM, Zhang SC. Sum-frequency vibrational spectroscopy of centrosymmetric molecule at interfaces. J Chem Phys 2023; 158:074701. [PMID: 36813719 DOI: 10.1063/5.0139895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The centrosymmetric benzene molecule has zero first-order electric dipole hyperpolarizability, which results in no sum-frequency vibrational spectroscopy (SFVS) signal at interfaces, but it shows very strong SFVS experimentally. We perform a theoretical study on its SFVS, which is in good agreement with the experimental results. Its strong SFVS mainly comes from the interfacial electric quadrupole hyperpolarizability rather than the symmetry-breaking electric dipole, bulk electric quadrupole, and interfacial and bulk magnetic dipole hyperpolarizabilities, which provides a novel and completely unconventional point of view.
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Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, People's Republic of China
| | - Wen-Mei Wei
- Department of Chemistry, College of Basic Medicine, Anhui Medical University, Hefei, Anhui 230032, People's Republic of China
| | - Shuo-Cang Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, People's Republic of China
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22
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Mousazadehkasin M, Mitchell N, Asenath-Smith E, Tsavalas JG. Ice Nucleation Promotion Impact on the Ice Recrystallization Inhibition Activity of Polyols. Biomacromolecules 2023; 24:678-689. [PMID: 36648113 DOI: 10.1021/acs.biomac.2c01120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Heterogeneous ice nucleation occurs vis-à-vis nucleating agents already present in solution yet can occur within a rather broad range of temperatures (0 to ca. -38 °C). Controlling this temperature and the subsequent growth of resulting ice crystals is crucial for the survival of biological organisms (certain insects, fish, and plants that endure subzero temperatures), as well as in the context of medical cryopreservation and food science. In these environments, uncontrolled crystal shape and size can rupture the cell membrane causing irreversible and catastrophic damage. Antifreeze (AF) proteins and synthetic AF analogs address this issue to restrict crystal growth and to shape ice crystals. Yet, if the nucleation temperature is not controlled and occurs in a lower temperature range, nascent ice crystals will have grown to a significantly larger size before the AF agents can be active on their surface to halt or slow the Ostwald ripening process during recrystallization. At a higher nucleation temperature, diffusion of AF macromolecules is enhanced, and dynamic crystal shaping can start earlier, producing smaller crystals overall. While antifreeze proteins, the inspiration for these synthetic analogs, are always applied in a salt buffer aqueous environment (most typically phosphate-buffered saline (PBS) buffer), the heterogeneous nucleation events are stochastic and occur within a wide temperature range. Silver iodide (AgI), however, is a highly effective ice nucleation promoter as its crystal lattice structure is a 98% lattice match to the basal plane of hexagonal ice (Ih) crystals acting as a template for water molecule orientation and decreasing the interfacial free energy. Here, we expose the advantage of purposely seeding such nascent ice crystals with AgI at a defined and higher temperature (-7 °C) in ultrapure water (UPW) such that nucleation can only come from AgI (and also in AgI/PBS), resulting in the most potent synthetic IRI observed to date (at concentrations as low as 0.001 mg·mL-1).
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Affiliation(s)
- Mohammad Mousazadehkasin
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Nick Mitchell
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Emily Asenath-Smith
- Cold Regions Research and Engineering Laboratory, US Army Engineer Research and Development Center, Hanover, New Hampshire 03755, United States
| | - John G Tsavalas
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States.,Materials Science Program, University of New Hampshire, Durham, New Hampshire 03824, United States
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23
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Fu Y, Li Y, Weng S, Qi W, Su H, Li T. Amyloid protein fibrils show enhanced ice recrystallization inhibition activity when serve as pickering emulsion stabilizer. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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24
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Fu Y, Li Y, Su H, Wu T, Li T. Inhibiting ice recrystallization by amyloid protein fibrils. Int J Biol Macromol 2023; 227:1132-1140. [PMID: 36470434 DOI: 10.1016/j.ijbiomac.2022.11.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/13/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022]
Abstract
Ice recrystallization is harmful to the quality of frozen foods and the cryopreservation of cells and biological tissues, requiring biocompatible materials with ice recrystallization inhibition (IRI) activity. Emerging studies have associated IRI activity with amphiphilic structures. We propose amphiphilic amyloid protein fibrils (APFs) may be IRI-active. APFs were prepared from whey protein isolate (WPI) in water (W-APFs) and in trifluoroethanol (TFE-APFs). W-APFs and TFE-APFs were more IRI-active than WPI over a concentration range of 2.5-10.0 mg/mL. Both APFs showed stronger IRI activity at pH 3.0 than at pH 5.0, 7.0, and 10.0, which was ascribed to the effect of water dispersibility and fibril length. The reduced IRI activity of the two APFs with increasing NaCl content was caused by fibril aggregation. Ice binding by APFs was absent or very weak. Ordered water was observed for the two APFs, which might be essential for IRI activity. Our findings may lead to the use of APFs as novel ice recrystallization inhibitors.
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Affiliation(s)
- Yuying Fu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yuan Li
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Huanhuan Su
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Tao Wu
- Department of Food Science, University of Tennessee, 2510 River Drive, Knoxville, TN 37996, USA
| | - Teng Li
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.
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Kozjek M, Vengust D, Radošević T, Žitko G, Koren S, Toplak N, Jerman I, Butala M, Podlogar M, Viršek MK. Dissecting giant hailstones: A glimpse into the troposphere with its diverse bacterial communities and fibrous microplastics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158786. [PMID: 36116646 DOI: 10.1016/j.scitotenv.2022.158786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/02/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The formation of giant hailstones is a rare weather event that has devastating consequences in inhabited areas. This hazard has been occurring more frequently and with greater size of hailstones in recent years, and thus needs to be better understood. While the generally accepted mechanism is thought to be a process similar to the formation of smaller hailstones but with exceptional duration and stronger updrafts, recent evidence suggests that biotic and abiotic factors also influence the growth of these unusually large ice chunks. In this study, we improved these findings by determining the distribution of a wide variety of these factors throughout the hail volume and expanding the search to include new particles that are common in the environment and are of anthropogenic origin. We melted the concentric layers of several giant hailstones that fell to the ground over a small region in Slovenia in 2019. The samples, up to 13 cm in diameter, were analyzed for biotic and abiotic constituents that could have influenced their formation. Using 16S rRNA-based metagenomics approaches, we identified a highly diverse bacterial community, and by using scanning electron microscopy and Raman spectroscopy, we found natural and synthetic fibers concentrated in the cores of the giant hailstones. For the first time, we were able to detect the existence of microplastic fibers in giant hailstones and determine the changes in the distribution of sand within the volume of the samples. Our results suggest that changes in the composition of hail layers and their great diversity are important factors that should be considered in research. It also appears that anthropogenic microfiber pollutants were a significant factor in the formation of the giant hailstones analyzed in this study.
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Affiliation(s)
- Marko Kozjek
- Institute for water of the Republic of Slovenia, Einspielerjeva 6, 1000 Ljubljana, Slovenia; University of Ljubljana, Biotechnical Faculty, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Damjan Vengust
- Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Tina Radošević
- Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Gregor Žitko
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia; National institute for chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
| | - Simon Koren
- Omega d.o.o., Dolinškova ulica 8, 1000 Ljubljana, Slovenia
| | - Nataša Toplak
- Omega d.o.o., Dolinškova ulica 8, 1000 Ljubljana, Slovenia
| | - Ivan Jerman
- National institute for chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
| | - Matej Butala
- University of Ljubljana, Biotechnical Faculty, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Matejka Podlogar
- Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Manca Kovač Viršek
- Institute for water of the Republic of Slovenia, Einspielerjeva 6, 1000 Ljubljana, Slovenia.
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Effect of active ice nucleation bacteria on freezing and the properties of surimi during frozen storage. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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27
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Wang Z, Li M, Wu T. Ice recrystallization inhibition activity in bile salts. J Colloid Interface Sci 2023; 629:728-738. [PMID: 36193617 DOI: 10.1016/j.jcis.2022.09.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022]
Abstract
Ice recrystallization inhibitors are novel cryoprotective agents that can reduce the freezing damage of cells, tissues, and organs in cryopreservation. To date, potent ice recrystallization inhibition (IRI) activity has been found on antifreeze (glyco)proteins, polymers, nanomaterials, and a limited number of chemically synthesized small molecules. This paper reports a relatively potent IRI activity on a group of small biological molecules - bile salts. The IRI activity increased as the number of hydroxyl groups decreased in bile salts. Among sodium cholate (NaC), sodium deoxycholate (NaDC), sodium chenodeoxycholate (NaCC), and sodium lithocholate (NaLC), the least hydrophilic NaLC at a concentration of 25.0 mM entirely blocked the ice growth in phosphate-buffered saline (PBS) under test conditions. The IRI activity of bile salts was not related to viscosity or gelation. No IRI activity was found below the critical micelle concentration. The IRI activity was independent of liquid crystal formation. No ice shaping and thermal hysteresis were observed on any bile salts, but NaC and NaLC could increase the ice nucleation temperature. The findings add bile salts to the existing material list of ice recrystallization inhibitors.
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Affiliation(s)
- Zhihong Wang
- Department of Food Science, The University of Tennessee, Knoxville, 2510 River Drive, TN 37996, USA
| | - Min Li
- Department of Food Science, The University of Tennessee, Knoxville, 2510 River Drive, TN 37996, USA
| | - Tao Wu
- Department of Food Science, The University of Tennessee, Knoxville, 2510 River Drive, TN 37996, USA.
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28
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Lin M, Cao H, Li J. Control strategies of ice nucleation, growth, and recrystallization for cryopreservation. Acta Biomater 2023; 155:35-56. [PMID: 36323355 DOI: 10.1016/j.actbio.2022.10.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 02/02/2023]
Abstract
The cryopreservation of biomaterials is fundamental to modern biotechnology and biomedicine, but the biggest challenge is the formation of ice, resulting in fatal cryoinjury to biomaterials. To date, abundant ice control strategies have been utilized to inhibit ice formation and thus improve cryopreservation efficiency. This review focuses on the mechanisms of existing control strategies regulating ice formation and the corresponding applications to biomaterial cryopreservation, which are of guiding significance for the development of ice control strategies. Herein, basics related to biomaterial cryopreservation are introduced first. Then, the theoretical bases of ice nucleation, growth, and recrystallization are presented, from which the key factors affecting each process are analyzed, respectively. Ice nucleation is mainly affected by melting temperature, interfacial tension, shape factor, and kinetic prefactor, and ice growth is mainly affected by solution viscosity and cooling/warming rate, while ice recrystallization is inhibited by adsorption or diffusion mechanisms. Furthermore, the corresponding research methods and specific control strategies for each process are summarized. The review ends with an outlook of the current challenges and future perspectives in cryopreservation. STATEMENT OF SIGNIFICANCE: Ice formation is the major limitation of cryopreservation, which causes fatal cryoinjury to cryopreserved biomaterials. This review focuses on the three processes related to ice formation, called nucleation, growth, and recrystallization. The theoretical models, key influencing factors, research methods and corresponding ice control strategies of each process are summarized and discussed, respectively. The systematic introduction on mechanisms and control strategies of ice formation is instructive for the cryopreservation development.
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Affiliation(s)
- Min Lin
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for CO(2) Utilization and Reduction Technology, Tsinghua University, Beijing 100084, China
| | - Haishan Cao
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for CO(2) Utilization and Reduction Technology, Tsinghua University, Beijing 100084, China.
| | - Junming Li
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for CO(2) Utilization and Reduction Technology, Tsinghua University, Beijing 100084, China
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29
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Ammann M, Artiglia L. Solvation, Surface Propensity, and Chemical Reactions of Solutes at Atmospheric Liquid-Vapor Interfaces. Acc Chem Res 2022; 55:3641-3651. [PMID: 36472357 PMCID: PMC9774673 DOI: 10.1021/acs.accounts.2c00604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
surface is covered by oceans, a large number of liquid aerosol particles fill the air, and clouds hold a tiny but critical fraction of Earth's water in the air to influence our climate and hydrology, enabling the lives of humans and ecosystems. The surfaces of these liquids provide the interface for the transfer of gases, for nucleation processes, and for catalyzing important chemical reactions. Coupling a range of spectroscopic tools to liquid microjets has become an important approach to better understanding dynamics, structure, and chemistry at liquid interfaces. Liquid microjets offer stability in vacuum and ambient pressure environments, thus also allowing X-ray photoelectron spectroscopy (XPS) with manageable efforts in terms of differential pumping. Liquid microjets are operated at speeds sufficient to allow for a locally equilibrated surface in terms of water dynamics and solute surface partitioning. XPS is based on the emission of core-level electrons, the binding energy of which is selective for the element and its chemical environment. Inelastic scattering of electrons establishes the probing depth of XPS in the nanometer range and thus its surface sensitivity.In this Account, we focus on aqueous solutions relevant to the surface of oceans, aqueous aerosols, or cloudwater. We are interested in understanding solvation and acid dissociation at the interface, interfacial aspects of reactions with gas-phase reactants, and the interplay of ions with organic molecules at the interface. The strategy is to obtain a link between the molecular-level picture and macroscopic properties and reactivity in the atmospheric context.We show consistency between surface tension and XPS for a range of surface-active organic species as an important proof for interrogating an equilibrated liquid surface. Measurements with organic acids and amines offer important insight into the question of apparent acidity or basicity at the interface. Liquid microjet XPS has settled the debate of the surface enhancement of halide ions, shown using the example of bromide and its oxidation products. Despite the absence of a strong enhancement for the bromide ion, its rate of oxidation by ozone is surface catalyzed through the stabilization of the bromide ozonide intermediate at the interface. In another reaction system, the one between Fe2+ and H2O2, a similar intermediate in the form of highly valent iron species could not be detected by XPS under the experimental conditions employed, shedding light on the abundance of this intermediate in the environment but also on the constraints within which surface species can be detected. Emphasizing the importance of electrostatic effects, we show how a cationic surfactant attracts charged bromide anions to the interface, accompanied by enhanced oxidation rates by ozone, overriding the role of surfactants as a barrier for the access of gas-phase reactants. The reactivity and structure at interfaces thus result from a subtle balance between hygroscopic and hydrophobic interactions, electrostatic effects, and the structural properties of both liquids and solutes.
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Yang H, Gladich I, Boucly A, Artiglia L, Ammann M. Orcinol and resorcinol induce local ordering of water molecules near the liquid-vapor interface. ENVIRONMENTAL SCIENCE: ATMOSPHERES 2022; 2:1277-1291. [PMID: 36561553 PMCID: PMC9648629 DOI: 10.1039/d2ea00015f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/17/2022] [Indexed: 12/25/2022]
Abstract
Resorcinol and orcinol are simple members of the family of phenolic compounds present in particulate matter in the atmosphere; they are amphiphilic in nature and thus surface active in aqueous solution. Here, we used X-ray photoelectron spectroscopy to probe the concentration of resorcinol (benzene-1,3-diol) and orcinol (5-methylbenzene-1,3-diol) at the liquid-vapor interface of aqueous solutions. Qualitatively consistent surface propensity and preferential orientation was obtained by molecular dynamics simulations. Auger electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy was used to probe the hydrogen bonding (HB) structure, indicating that the local structure of water molecules near the surface of the resorcinol and orcinol solutions tends towards a larger fraction of tetrahedrally coordinated molecules than observed at the liquid-vapor interface of pure water. The order parameter obtained from the molecular dynamics simulations confirm these observations. This effect is being discussed in terms of the formation of an ordered structure of these molecules at the surface leading to patterns of hydrated OH groups with distances among them that are relatively close to those in ice. These results suggest that the self-assembly of phenolic species at the aqueous solution-air interface could induce freezing similar to the case of fatty alcohol monolayers and, thus, be of relevance for ice nucleation in the atmosphere. We also attempted at looking at the changes of the O 1b1, 3a2 and 1b2 molecular orbitals of liquid water, which are known to be sensitive to the HB structure as well, in response to the presence of resorcinol and orcinol. However, these changes remained negligible within uncertainty for both experimentally obtained valence spectra and theoretically calculated density of states.
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Affiliation(s)
- Huanyu Yang
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland,Institute of Atmospheric and Climate Science, ETH Zürich8092 ZürichSwitzerland
| | - Ivan Gladich
- Qatar Environment & Energy Research Institute, Hamad Bin Khalifa UniversityP.O. Box 34110DohaQatar
| | - Anthony Boucly
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland,Electrochemistry Laboratory, Paul Scherrer Institut5232 VilligenSwitzerland
| | - Luca Artiglia
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland,Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland
| | - Markus Ammann
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland
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31
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Zhang X, Maeda N. Nucleation curves of ice in the presence of nucleation promoters. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Electron microscopy and calorimetry of proteins in supercooled water. Sci Rep 2022; 12:16512. [PMID: 36192511 PMCID: PMC9529883 DOI: 10.1038/s41598-022-20430-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/13/2022] [Indexed: 11/08/2022] Open
Abstract
Some of the best nucleating agents in nature are ice-nucleating proteins, which boost ice growth better than any other material. They can induce immersion freezing of supercooled water only a few degrees below 0 °C. An open question is whether this ability also extends to the deposition mode, i.e., to water vapor. In this work, we used three proteins, apoferritin, InaZ (ice nucleation active protein Z), and myoglobin, of which the first two are classified as ice-nucleating proteins for the immersion freezing mode. We studied the ice nucleation ability of these proteins by differential scanning calorimetry (immersion freezing) and by environmental scanning electron microscopy (deposition freezing). Our data show that InaZ crystallizes water directly from the vapor phase, while apoferritin first condenses water in the supercooled state, and subsequently crystallizes it, just as myoglobin, which is unable to nucleate ice.
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Identification of Candidate Ice Nucleation Activity (INA) Genes in Fusarium avenaceum by Combining Phenotypic Characterization with Comparative Genomics and Transcriptomics. J Fungi (Basel) 2022; 8:jof8090958. [PMID: 36135683 PMCID: PMC9501429 DOI: 10.3390/jof8090958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022] Open
Abstract
Ice nucleation activity (INA) is the capacity of certain particles to catalyze ice formation at temperatures higher than the temperature at which pure water freezes. INA impacts the ratio of liquid to frozen cloud droplets and, therefore, the formation of precipitation and Earth’s radiative balance. Some Fusarium strains secrete ice-nucleating particles (INPs); they travel through the atmosphere and may thus contribute to these atmospheric processes. Fusarium INPs were previously found to consist of proteinaceous aggregates. Here, we determined that in F. avenaceum, the proteins forming these aggregates are smaller than 5 nm and INA is higher after growth at low temperatures and varies among strains. Leveraging these findings, we used comparative genomics and transcriptomics to identify candidate INA genes. Ten candidate INA genes that were predicted to encode secreted proteins were present only in the strains that produced the highest number of INPs. In total, 203 candidate INA genes coding for secreted proteins were induced at low temperatures. Among them, two genes predicted to encode hydrophobins stood out because hydrophobins are small, secreted proteins that form aggregates with amphipathic properties. We discuss the potential of the candidate genes to encode INA proteins and the next steps necessary to identify the molecular basis of INA in F. avenaceum.
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34
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Deep learning for unravelling features of heterogeneous ice nucleation. Proc Natl Acad Sci U S A 2022; 119:e2211295119. [PMID: 35981133 PMCID: PMC9436343 DOI: 10.1073/pnas.2211295119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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35
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Water-organizing motif continuity is critical for potent ice nucleation protein activity. Nat Commun 2022; 13:5019. [PMID: 36028506 PMCID: PMC9418140 DOI: 10.1038/s41467-022-32469-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency. Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.
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36
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Wen Q, Duan J, Wang W, Huang D, Liu Y, Shi Y, Fang J, Nie A, Li H, Zhai T. Engineering a Local Free Water Enriched Microenvironment for Surpassing Platinum Hydrogen Evolution Activity. Angew Chem Int Ed Engl 2022; 61:e202206077. [DOI: 10.1002/anie.202206077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Qunlei Wen
- State Key Laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Junyuan Duan
- State Key Laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Wenbin Wang
- State Key Laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Danji Huang
- State Key Lab of Advanced Electromagnetic Engineering and Technology School of Electrical and Electronic Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Youwen Liu
- State Key Laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Yongliang Shi
- Center for Spintronics and Quantum Systems, State Key Laboratory for Mechanical Behavior of Materials School of Materials Science and Engineering Xi'an Jiaotong University Xi'an Shanxi, 710049 P. R. China
| | - JiaKun Fang
- State Key Lab of Advanced Electromagnetic Engineering and Technology School of Electrical and Electronic Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Anmin Nie
- Center for High Pressure Science State Key Laboratory of Metastable Materials Science and Technology Yanshan University Qinhuangdao Hebei, 066004 P. R. China
| | - Huiqiao Li
- State Key Laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
| | - Tianyou Zhai
- State Key Laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology Wuhan Hubei, 430074 P. R. China
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37
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Chatterley AS, Golbek TW, Weidner T. Measuring Protein Conformation at Aqueous Interfaces with 2D Infrared Spectroscopy of Emulsions. J Phys Chem Lett 2022; 13:7191-7196. [PMID: 35905449 DOI: 10.1021/acs.jpclett.2c01324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Determining the secondary and tertiary structures of proteins at aqueous interfaces is crucial for understanding their function, but measuring these structures selectively at the interface is challenging. Here we demonstrate that two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions offers a new route to measuring interfacial protein structure with high levels of detail. We prepared hexadecane/water oil-in-water emulsions stabilized by model LK peptides that are known to fold into either α-helix or β-sheet conformations at hydrophobic interfaces and measured 2D-IR spectra in a transmission geometry. We saw clear spectral signatures of the peptides folding at the interface, with no detectable residue from remaining bulk peptides. Using 2D spectroscopy gives us access to correlation and dynamics data, which enables structural assignment in cases where linear spectroscopy fails. Using the emulsions allows one to study interfacial spectra with standard transmission geometry spectrometers, bringing the richness of 2D-IR to the interface with no additional optical complexity.
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Affiliation(s)
| | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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38
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Avalos-Ruiz D, Ten LN, Kim CK, Lee SY, Jung HY. Isolation and Identification of Ice Nucleation Active Fusarium Strains from Rapid Apple Declined Trees in Korea. THE PLANT PATHOLOGY JOURNAL 2022; 38:403-409. [PMID: 35953060 PMCID: PMC9372094 DOI: 10.5423/ppj.nt.04.2022.0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
In biological particles such as Fusarium species, ice nucleation activity (INA) has been observed. Fusarium strains isolated from apple declined trees in Korea were identified with a multilocus sequence analysis using the tef1 and rpb1 genes. Droplet-freezing and tube-freezing assays were used to determine the INA of the strains, using Pseudomonas syringae pv. syringae KACC 21200 as a positive control and resulting in seven INA+ fungal strains that were identified as F. tricinctum (KNUF- 21-F17, KNUF-21-F18, KNUF-21-F29, KNUF-21-F32, KNUF-21-F38, KNUF-21-F43, and KNUF-21-F44). The effect of Fusarium INA+ KNUF-21-F29 was compared to that of INA- strains on Chrysanthemum morifolium cv. Shinma explants. A higher callus formation and noshoot formation were observed, suggesting that fungal INA could play a role in cold injuries and be a factor to consider in rapid apple decline. To the best of our knowledge, this is the first report of INA fungal strains isolated in Korea.
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Affiliation(s)
- Diane Avalos-Ruiz
- School of Applied Biosciences, Kyungpook National University, Daegu 41566,
Korea
| | - Leonid N. Ten
- School of Applied Biosciences, Kyungpook National University, Daegu 41566,
Korea
| | - Chang-Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566,
Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566,
Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566,
Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566,
Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566,
Korea
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39
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Lu H, Bellucci L, Sun S, Qi D, Rosa M, Berger R, Corni S, Bonn M. Acidic pH Promotes Refolding and Macroscopic Assembly of Amyloid β (16-22) Peptides at the Air-Water Interface. J Phys Chem Lett 2022; 13:6674-6679. [PMID: 35839425 PMCID: PMC9340808 DOI: 10.1021/acs.jpclett.2c01171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/12/2022] [Indexed: 05/31/2023]
Abstract
Assembly by amyloid-beta (Aβ) peptides is vital for various neurodegenerative diseases. The process can be accelerated by hydrophobic interfaces such as the cell membrane interface and the air-water interface. Elucidating the assembly mechanism for Aβ peptides at hydrophobic interface requires knowledge of the microscopic structure of interfacial peptides. Here we combine scanning force microscopy, sum-frequency generation spectroscopy, and metadynamics simulations to probe the structure of the central fragment of Aβ peptides at the air-water interface. We find that the structure of interfacial peptides depends on pH: at neutral pH, the peptides adopt a less folded, bending motif by forming intra-hydrogen bonds; at acidic pH, the peptides refold into extended β-strand fibril conformation, which further promotes their macroscopic assembly. The conformational transition of interfacial peptides is driven by the reduced hydrogen bonds, both with water and within peptides, resulting from the protonation of acidic glutamic acid side chains.
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Affiliation(s)
- Hao Lu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Luca Bellucci
- NEST
− Istituto di Nanoscienze del Consiglio Nazionale delle Ricerche
CNR-NANO and Scuola Normale Superiore, Piazza S. Silvestro 12, Pisa, 56127, Italy
| | - Shumei Sun
- Department
of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Daizong Qi
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marta Rosa
- Istituto
di Nanoscienze del Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
- Dipartimento
di Scienze Chimiche, Università di
Padova, 35131 Padova, Italy
| | - Rüdiger Berger
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Stefano Corni
- Istituto
di Nanoscienze del Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
- Dipartimento
di Scienze Chimiche, Università di
Padova, 35131 Padova, Italy
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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Gebauer D, Gale JD, Cölfen H. Crystal Nucleation and Growth of Inorganic Ionic Materials from Aqueous Solution: Selected Recent Developments, and Implications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107735. [PMID: 35678091 DOI: 10.1002/smll.202107735] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/07/2022] [Indexed: 05/27/2023]
Abstract
In this review article, selected, latest theoretical, and experimental developments in the field of nucleation and crystal growth of inorganic materials from aqueous solution are highlighted, with a focus on literature after 2015 and on non-classical pathways. A key point is to emphasize the so far underappreciated role of water and solvent entropy in crystallization at all stages from solution speciation through to the final crystal. While drawing on examples from current inorganic materials where non-classical behavior has been proposed, the potential of these approaches to be adapted to a wide-range of systems is also discussed, while considering the broader implications of the current re-assessment of pathways for crystallization. Various techniques that are suitable for the exploration of crystallization pathways in aqueous solution, from nucleation to crystal growth are summarized, and a flow chart for the assignment of specific theories based on experimental observations is proposed.
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Affiliation(s)
- Denis Gebauer
- Leibniz University Hannover, Institute of Inorganic Chemistry, Callinstr. 9, 30167, Hannover, Germany
| | - Julian D Gale
- Curtin Institute for Computation/The Institute for Geoscience Research (TiGER), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia, 6845, Australia
| | - Helmut Cölfen
- University of Konstanz, Physical Chemistry, Universitätsstr. 10, 78465, Konstanz, Germany
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42
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Wen Q, Duan J, Wang W, Huang D, Liu Y, Shi Y, Fang J, Nie A, Li H, Zhai T. Engineering a Local Free Water Enriched Microenvironment for Surpassing Platinum Hydrogen Evolution Activity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qunlei Wen
- Huazhong University of Science and Technology School of Material Science and Engineering CHINA
| | - Junyuan Duan
- Huazhong University of Science and Technology School of Material Science and Engineering CHINA
| | - Wenbin Wang
- Huazhong University of Science and Technology School of Material Science and Engineering CHINA
| | - Danji Huang
- Huazhong University of Science and Technology School of Electrical and Eltctronic Engineering CHINA
| | - Youwen Liu
- Huazhong University of Science and Technology School of Material Science and Engineering CHINA
| | - Yongliang Shi
- Xi'an Jiaotong University School of Material Science and Engineering CHINA
| | - Jiakun Fang
- Huazhong University of Science and Technology School of Electrical and Eltctronic Engineering CHINA
| | - Anmin Nie
- Yanshan University School of Material Science and Engineering CHINA
| | - Huiqiao Li
- Huazhong University of Science and Technology School of Material Science and Engineering CHINA
| | - Tianyou Zhai
- Huazhong University of Science and Technology - Main Campus: Huazhong University of Science and Technology Luoyu Road 430074 Wuhan CHINA
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43
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Hartmann S, Ling M, Dreyer LSA, Zipori A, Finster K, Grawe S, Jensen LZ, Borck S, Reicher N, Drace T, Niedermeier D, Jones NC, Hoffmann SV, Wex H, Rudich Y, Boesen T, Šantl-Temkiv T. Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity. Front Microbiol 2022; 13:872306. [PMID: 35783412 PMCID: PMC9247515 DOI: 10.3389/fmicb.2022.872306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Airborne microorganisms utilize these proteins to enhance their survival by reducing their atmospheric residence times. INpro also have critical environmental effects including impacts on the atmospheric water cycle, through their role in cloud and precipitation formation, as well as frost damage on crops. INpro are ubiquitously present in the atmosphere where they are emitted from diverse terrestrial and marine environments. Even though bacterial genes encoding INpro have been discovered and sequenced decades ago, the details of how the INpro molecular structure and oligomerization foster their unique ice-nucleation activity remain elusive. Using machine-learning based software AlphaFold 2 and trRosetta, we obtained and analysed the first ab initio structural models of full length and truncated versions of bacterial INpro. The modeling revealed a novel beta-helix structure of the INpro central repeat domain responsible for ice nucleation activity. This domain consists of repeated stacks of two beta strands connected by two sharp turns. One beta-strand is decorated with a TxT amino acid sequence motif and the other strand has an SxL[T/I] motif. The core formed between the stacked beta helix-pairs is unusually polar and very distinct from previous INpro models. Using synchrotron radiation circular dichroism, we validated the β-strand content of the central repeat domain in the model. Combining the structural model with functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. Using computational docking of the new INpro model based on rigid-body algorithms we could reproduce a previously proposed homodimer structure of the INpro CRD with an interface along a highly conserved tyrosine ladder and show that the dimer model agrees with our functional data. The parallel dimer structure creates a surface where the TxT motif of one monomer aligns with the SxL[T/I] motif of the other monomer widening the surface that interacts with water molecules and therefore enhancing the ice nucleation activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity.
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Affiliation(s)
| | - Meilee Ling
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Lasse S. A. Dreyer
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Assaf Zipori
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kai Finster
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
| | - Sarah Grawe
- Institute for Tropospheric Research, Leipzig, Germany
| | - Lasse Z. Jensen
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Stella Borck
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Naama Reicher
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Taner Drace
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | | | - Nykola C. Jones
- Department of Physics and Astronomy, The Institute for Storage Ring Facilities, Aarhus University, Aarhus, Denmark
| | - Søren V. Hoffmann
- Department of Physics and Astronomy, The Institute for Storage Ring Facilities, Aarhus University, Aarhus, Denmark
| | - Heike Wex
- Institute for Tropospheric Research, Leipzig, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center and Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Thomas Boesen,
| | - Tina Šantl-Temkiv
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- *Correspondence: Tina Šantl-Temkiv,
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44
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Khosasih V, Prasetyo N, Sudianto E, Waturangi DE. Prevalence and characterization of Ice Nucleation Active (INA) bacteria from rainwater in Indonesia. BMC Microbiol 2022; 22:116. [PMID: 35477335 PMCID: PMC9044597 DOI: 10.1186/s12866-022-02521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ice nucleation active (INA) bacteria are a group of microorganisms that can act as biological nucleator due to their ice nucleation protein property. Unfortunately, little is known about their prevalence and characteristics in tropical areas including Indonesia. Here, we monitor the presence of INA bacteria in rainwater and air samples collected from Jakarta, Tangerang and several areas in Western Java, Indonesia for one year. We further identify and characterize selected Class A of INA bacteria isolated from these areas. Results Most of the INA bacteria were isolated from rainwater samples collected during March–August 2010, particularly from Jakarta, Bandung, and Tangerang. A total of 1,902 bacterial isolates were recovered from these area. We found a limited number of bacterial isolates from air sampling. From ice nucleation activity assays, 101 INA isolates were found active as ice nucleator at a temperature above -10 °C. A large majority (73 isolates) of them are classified as Class C (active below -8 °C), followed by Class A (26 isolates; active at -2 to -5 °C) and Class B (two isolates; active at -5 to -8 °C). We sequenced the 16S rRNA gene of 18 Class A INA isolates and identified 15 isolates as Enterobacteriaceae, while the remaining three as Pseudomonadaceae. The vast majority of our Class A INA isolates were likely Pantoea spp. with several isolates were deduced as either Pseudomonas, Cronobacter, and Klebsiella. We found that these 18 Class A INA isolates had acquired resistance to antibiotics erythromycin and ampicillin, which are considered two critically important antibiotics. Conclusions Our results showed that the prevalence of INA bacterial population varies across locations and seasons. Furthermore, our isolates were dominated by Class A and C INA bacteria. This study also cautions regarding the spread of antibiotic resistance among INA bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02521-1.
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Affiliation(s)
- Vivia Khosasih
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman, Jakarta, 12930, Indonesia.,Present Address: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, 115
| | - Niko Prasetyo
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman, Jakarta, 12930, Indonesia
| | - Edi Sudianto
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 701
| | - Diana Elizabeth Waturangi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman, Jakarta, 12930, Indonesia.
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45
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Lukas M, Backus EHG, Bonn M, Grechko M. Passively Stabilized Phase-Resolved Collinear SFG Spectroscopy Using a Displaced Sagnac Interferometer. J Phys Chem A 2022; 126:951-956. [PMID: 35113564 DOI: 10.1021/acs.jpca.1c10155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sum-frequency generation (SFG) vibrational spectroscopy is a powerful technique to study interfaces at the molecular level. Phase-resolved SFG (PR-SFG) spectroscopy provides direct information on interfacial molecules' orientation. However, its implementation is technologically demanding: it requires the generation of a local oscillator wave and control of its time delay with sub-fs accuracy. Commonly used noncollinear PR-SFG provides this control naturally but requires very accurate sample height control. Collinear PR-SFG spectroscopy is less demanding regarding sample positioning, but tuning the local oscillator time delay with this beam geometry is challenging. Here, we develop a collinear PR-SFG setup using a displaced Sagnac interferometer. This scheme allows full, independent control of the time delay and intensity of the local oscillator and provides long-time phase stabilization (better than 5° over 12 h) for the measured signal. This approach substantially reduces the complexity of an experimental setup and combines the advantages of collinear and noncollinear PR-SFG techniques.
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Affiliation(s)
- Max Lukas
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Ellen H G Backus
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany.,Department of Physical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Maksim Grechko
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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46
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Vachier J, Wettlaufer JS. Premelting controlled active matter in ice. Phys Rev E 2022; 105:024601. [PMID: 35291135 DOI: 10.1103/physreve.105.024601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Self-propelled particles can undergo complex dynamics due to a range of bulk and surface interactions. When a particle is embedded in a host solid near its bulk melting temperature, the latter may melt at the surface of the former in a process known as interfacial premelting. The thickness of the melt film depends on the temperature, impurities, material properties and geometry. A temperature gradient is accompanied by a thermomolecular pressure gradient that drives the interfacial liquid from high to low temperatures and hence the particle from low to high temperatures, in a process called thermal regelation. When the host material is ice and the embedded particle is a biological entity, one has a particularly different form of active matter, which addresses interplay between a wide range of problems, from extremophiles of both terrestrial and exobiological relevance to ecological dynamics in Earth's cryosphere. Of basic importance in all such settings is the combined influence of biological activity and thermal regelation in controlling the redistribution of bioparticles. Therefore, we recast this class of regelation phenomena in the stochastic framework of active Ornstein-Uhlenbeck dynamics and make predictions relevant to this and related problems of interest in biological and geophysical problems. We examine how thermal regelation compromises paleoclimate studies in the context of ice core dating and we find that the activity influences particle dynamics during thermal regelation by enhancing the effective diffusion coefficient. Therefore, accurate dating relies on a quantitative treatment of both effects.
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Affiliation(s)
- Jérémy Vachier
- Nordita, KTH Royal Institute of Technology and Stockholm University, Hannes Alfvéns väg 12, SE-106 91 Stockholm, Sweden
| | - J S Wettlaufer
- Nordita, KTH Royal Institute of Technology and Stockholm University, Hannes Alfvéns väg 12, SE-106 91 Stockholm, Sweden
- Yale University, New Haven, Connecticut 06520-8109, USA
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47
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Lukas M, Schwidetzky R, Eufemio RJ, Bonn M, Meister K. Toward Understanding Bacterial Ice Nucleation. J Phys Chem B 2022; 126:1861-1867. [PMID: 35084861 PMCID: PMC8919256 DOI: 10.1021/acs.jpcb.1c09342] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Bacterial ice nucleators
(INs) are among the most effective ice
nucleators known and are relevant for freezing processes in agriculture,
the atmosphere, and the biosphere. Their ability to facilitate ice
formation is due to specialized ice-nucleating proteins (INPs) anchored
to the outer bacterial cell membrane, enabling the crystallization
of water at temperatures up to −2 °C. In this Perspective,
we highlight the importance of functional aggregation of INPs for
the exceptionally high ice nucleation activity of bacterial ice nucleators.
We emphasize that the bacterial cell membrane, as well as environmental
conditions, is crucial for a precise functional INP aggregation. Interdisciplinary
approaches combining high-throughput droplet freezing assays with
advanced physicochemical tools and protein biochemistry are needed
to link changes in protein structure or protein–water interactions
with changes on the functional level.
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Affiliation(s)
- Max Lukas
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | | | - Mischa Bonn
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Konrad Meister
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany.,University of Alaska Southeast, Juneau, Alaska 99801, United States
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48
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Surís-Valls R, Hogervorst TP, Schoenmakers SMC, Hendrix MMRM, Milroy L, Voets IK. Inhibition of Ice Recrystallization by Nanotube-Forming Cyclic Peptides. Biomacromolecules 2022; 23:520-529. [PMID: 35045706 PMCID: PMC8848283 DOI: 10.1021/acs.biomac.1c01267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While most native ice-binding proteins are rigid, artificial (macro)molecular ice-binders are usually flexible. Realizing a regular array with precisely positioned ice-binding motifs on synthetic proteins, (macro)molecular ice-binders are thus challenging. Here, we exploit the predictable assembly of cyclic peptides into nanotubes as a starting point to prepare large, rigid ice-binders bearing an ice-binding site that is found in hyperactive ice-binding proteins in insects. First, we designed, synthesized, and purified cyclic octapeptide Lys2CP8 bearing a TaT motif to promote ice binding and investigated their solution assembly and activity using circular dichroism (CD) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, light scattering (LS), cryogenic transmission electron microscopy (cryo-TEM), and ice recrystallization inhibition (IRI) assays. The cyclic peptide Lys2CP8 was synthesized in good yield using Fmoc chemistry and purified by reversed-phase HPLC. Upon dissolution in aqueous solutions, Lys2CP8 was observed to assemble in a pH- and concentration-dependent manner into objects with nanoscopic dimensions. LS revealed the presence of small and large aggregates at pH 3 and 11, held together through a network of intermolecular antiparallel β-sheets as determined by FTIR and CD spectroscopy. Cryo-TEM revealed the presence of one-dimensional objects at pH 3 and 11. These are mostly well-dispersed at pH 3 but appear to bundle at pH 11. Interestingly, the pH-dependent self-assembly behavior translates into a marked pH dependence of IRI activity. Lys2CP8 is IRI-active at pH 3 while inactive at pH 11 hypothetically because the ice-binding sites are inaccessible at pH 11 due to bundling.
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Affiliation(s)
- Romà Surís-Valls
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Laboratory of Chemical Biology, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Tim P Hogervorst
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Sandra M C Schoenmakers
- Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Marco M R M Hendrix
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Lech Milroy
- Laboratory of Chemical Biology, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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49
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Zheng RH, Wei WM. Sum-frequency vibrational spectroscopy of methanol at interfaces due to Fermi resonance. Phys Chem Chem Phys 2022; 24:27204-27211. [DOI: 10.1039/d2cp01808j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We present a theoretical method of studying sum-frequency vibrational spectroscopy for the CH3 group of methanol at interfaces due to Fermi resonance, which provides a novel and untraditional point of view with respect to traditional approaches.
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Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, P. R. China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, Anhui, 230032, P. R. China
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50
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Šantl-Temkiv T, Amato P, Casamayor EO, Lee PKH, Pointing SB. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6524182. [PMID: 35137064 PMCID: PMC9249623 DOI: 10.1093/femsre/fuac009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.
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Affiliation(s)
- Tina Šantl-Temkiv
- Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont Auvergne, 63178, Clermont-Ferrand, France
| | - Emilio O Casamayor
- Centre for Advanced Studies of Blanes, Spanish Council for Research (CSIC), 17300, Blanes, Spain
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Stephen B Pointing
- Corresponding author: Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527. Tel: +65 6601 1000; E-mail:
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