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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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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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3
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Melnik BS, Glukhova KA, Sokolova (Voronova) EA, Balalaeva IV, Garbuzynskiy SO, Finkelstein AV. Physics of Ice Nucleation and Antinucleation: Action of Ice-Binding Proteins. Biomolecules 2023; 14:54. [PMID: 38254654 PMCID: PMC10813080 DOI: 10.3390/biom14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/09/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Ice-binding proteins are crucial for the adaptation of various organisms to low temperatures. Some of these, called antifreeze proteins, are usually thought to inhibit growth and/or recrystallization of ice crystals. However, prior to these events, ice must somehow appear in the organism, either coming from outside or forming inside it through the nucleation process. Unlike most other works, our paper is focused on ice nucleation and not on the behavior of the already-nucleated ice, its growth, etc. The nucleation kinetics is studied both theoretically and experimentally. In the theoretical section, special attention is paid to surfaces that bind ice stronger than water and thus can be "ice nucleators", potent or relatively weak; but without them, ice cannot be nucleated in any way in calm water at temperatures above -30 °C. For experimental studies, we used: (i) the ice-binding protein mIBP83, which is a previously constructed mutant of a spruce budworm Choristoneura fumiferana antifreeze protein, and (ii) a hyperactive ice-binding antifreeze protein, RmAFP1, from a longhorn beetle Rhagium mordax. We have shown that RmAFP1 (but not mIBP83) definitely decreased the ice nucleation temperature of water in test tubes (where ice originates at much higher temperatures than in bulk water and thus the process is affected by some ice-nucleating surfaces) and, most importantly, that both of the studied ice-binding proteins significantly decreased the ice nucleation temperature that had been significantly raised in the presence of potent ice nucleators (CuO powder and ice-nucleating bacteria Pseudomonas syringae). Additional experiments on human cells have shown that mIBP83 is concentrated in some cell regions of the cooled cells. Thus, the ice-binding protein interacts not only with ice, but also with other sites that act or potentially may act as ice nucleators. Such ice-preventing interaction may be the crucial biological task of ice-binding proteins.
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Affiliation(s)
- Bogdan S. Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Ksenia A. Glukhova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Evgeniya A. Sokolova (Voronova)
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Irina V. Balalaeva
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
- Faculty of Biotechnology, Lomonosov Moscow State University, 142290 Pushchino, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
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4
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Hansen T, Lee J, Reicher N, Ovadia G, Guo S, Guo W, Liu J, Braslavsky I, Rudich Y, Davies PL. Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C. eLife 2023; 12:RP91976. [PMID: 38109272 PMCID: PMC10727499 DOI: 10.7554/elife.91976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins (INPs) of common environmental bacteria like Pseudomonas syringae and Pseudomonas borealis. However, individually, these 100 kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an INP gene into Escherichia coli led to efficient ice nucleation. Here, we demonstrate that a positively charged subdomain at the C-terminal end of the central β-solenoid of the INP is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the INP multimers form fibres that are ~5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.
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Affiliation(s)
- Thomas Hansen
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Jocelyn Lee
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Naama Reicher
- Department of Earth and Planetary Sciences, The Weizmann Institute of ScienceRehovotIsrael
| | - Gil Ovadia
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of JerusalemRehovotIsrael
| | - Shuaiqi Guo
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of JerusalemRehovotIsrael
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, The Weizmann Institute of ScienceRehovotIsrael
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
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5
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Schwidetzky R, de Almeida Ribeiro I, Bothen N, Backes AT, DeVries AL, Bonn M, Fröhlich-Nowoisky J, Molinero V, Meister K. Functional aggregation of cell-free proteins enables fungal ice nucleation. Proc Natl Acad Sci U S A 2023; 120:e2303243120. [PMID: 37943838 PMCID: PMC10655213 DOI: 10.1073/pnas.2303243120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
Biological ice nucleation plays a key role in the survival of cold-adapted organisms. Several species of bacteria, fungi, and insects produce ice nucleators (INs) that enable ice formation at temperatures above -10 °C. Bacteria and fungi produce particularly potent INs that can promote water crystallization above -5 °C. Bacterial INs consist of extended protein units that aggregate to achieve superior functionality. Despite decades of research, the nature and identity of fungal INs remain elusive. Here, we combine ice nucleation measurements, physicochemical characterization, numerical modeling, and nucleation theory to shed light on the size and nature of the INs from the fungus Fusarium acuminatum. We find ice-binding and ice-shaping activity of Fusarium IN, suggesting a potential connection between ice growth promotion and inhibition. We demonstrate that fungal INs are composed of small 5.3 kDa protein subunits that assemble into ice-nucleating complexes that can contain more than 100 subunits. Fusarium INs retain high ice-nucleation activity even when only the ~12 kDa fraction of size-excluded proteins are initially present, suggesting robust pathways for their functional aggregation in cell-free aqueous environments. We conclude that the use of small proteins to build large assemblies is a common strategy among organisms to create potent biological INs.
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Affiliation(s)
- Ralph Schwidetzky
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz55128, Germany
| | | | - Nadine Bothen
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz55128, Germany
| | - Anna T. Backes
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz55128, Germany
| | - Arthur L. DeVries
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz55128, Germany
| | | | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, UT84112
| | - Konrad Meister
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz55128, Germany
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID83725
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6
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Hansen T, Lee JC, Reicher N, Ovadia G, Guo S, Guo W, Liu J, Braslavsky I, Rudich Y, Davies PL. Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551873. [PMID: 37577566 PMCID: PMC10418271 DOI: 10.1101/2023.08.03.551873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins of common environmental bacteria like Pseudomonas syringae and P. borealis. However, individually, these 100-kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an ice nucleation protein gene into Escherichia coli led to efficient ice nucleation. Here we demonstrate that a positively-charged sub-domain at the C-terminal end of the central beta-solenoid of the ice nucleation protein is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the ice nucleation protein multimers form fibres that are ~ 5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.
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Affiliation(s)
- Thomas Hansen
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON Canada K7L 3N6
| | - Jocelyn C. Lee
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON Canada K7L 3N6
| | - Naama Reicher
- Department of Earth and Planetary Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gil Ovadia
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Shuaiqi Guo
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON Canada K7L 3N6
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7
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Song R, Jiang C, Zhu J, Liu J, Zhang L, Zuo J, Zheng W, Liu S, Huang Q, Wei X, Chen Y. Expression of Ice Nucleation Protein in Bacillus amyloliquefaciens and Its Application in Food Freezing Process. Foods 2023; 12:3896. [PMID: 37959016 PMCID: PMC10650300 DOI: 10.3390/foods12213896] [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: 08/31/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023] Open
Abstract
To produce food-grade ice nucleators, a 3.77 kb ice nucleation gene (iceE) isolated from Pantoea agglomerans (Erwinia herbicola) was introduced into the Gram-positive microorganism Bacillus amyloliquefaciens for the first time. The differential scanning calorimetry (DSC) results indicated that recombined strain B9-INP was an effective ice nucleator for controlling the supercooling point of distilled water at low concentrations. In the presence of B9-INP cells, model food systems, including sucrose solution and sodium chloride solution, different pH solutions froze at a relatively high subzero temperature, thus increasing the supercooling point by 5.8~16.7 °C. Moreover, B9-INP also facilitated model and real food systems to freeze at -6 °C. This recombinant strain not only improved the freezing temperature of food systems but also shortened the total freezing time, thus saving energy and reducing consumption. The results suggest that B9-INP has great application potential in the frozen food industry.
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Affiliation(s)
- Rong Song
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Cong Jiang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zhu
- Hubei Institute of Measurement and Testing Technology, Wuhan 430070, China;
| | - Jia Liu
- College of Life Science, Yangtze University, Jingzhou 434023, China;
| | - Li Zhang
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; (L.Z.); (Q.H.)
| | - Jingnan Zuo
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zheng
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shilin Liu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingrong Huang
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; (L.Z.); (Q.H.)
| | - Xuetuan Wei
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yijie Chen
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, China; (R.S.); (C.J.); (J.Z.); (W.Z.); (S.L.); (X.W.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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8
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Amato P, Mathonat F, Nuñez Lopez L, Péguilhan R, Bourhane Z, Rossi F, Vyskocil J, Joly M, Ervens B. The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome. Front Microbiol 2023; 14:1186847. [PMID: 37260685 PMCID: PMC10227452 DOI: 10.3389/fmicb.2023.1186847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/24/2023] [Indexed: 06/02/2023] Open
Abstract
The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.
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Eickhoff L, Keßler M, Stubbs C, Derksen J, Viefhues M, Anselmetti D, Gibson MI, Hoge B, Koop T. Ice nucleation in aqueous solutions of short- and long-chain poly(vinyl alcohol) studied with a droplet microfluidics setup. J Chem Phys 2023; 158:2882248. [PMID: 37093996 DOI: 10.1063/5.0136192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/22/2023] [Indexed: 04/26/2023] Open
Abstract
Poly(vinyl alcohol) (PVA) has ice binding and ice nucleating properties. Here, we explore the dependence of the molecular size of PVA on its ice nucleation activity. For this purpose, we studied ice nucleation in aqueous solutions of PVA samples with molar masses ranging from 370 to 145 000 g mol-1, with a particular focus on oligomer samples with low molar mass. The experiments employed a novel microfluidic setup that is a follow-up on the previous WeIzmann Supercooled Droplets Observation on a Microarray (WISDOM) design by Reicher et al. The modified setup introduced and characterized here, termed nanoliter Bielefeld Ice Nucleation ARraY (nanoBINARY), uses droplet microfluidics with droplets (96 ± 4) µm in diameter and a fluorinated continuous oil phase and surfactant. A comparison of homogeneous and heterogeneous ice nucleation data obtained with nanoBINARY to those obtained with WISDOM shows very good agreement, underpinning its ability to study low-temperature ice nucleators as well as homogeneous ice nucleation due to the low background of impurities. The experiments on aqueous PVA solutions revealed that the ice nucleation activity of shorter PVA chains strongly decreases with a decrease in molar mass. While the cumulative number of ice nucleating sites per mass nm of polymers with different molar masses is the same, it becomes smaller for oligomers and completely vanishes for dimer and monomer representatives such as 1,3-butanediol, propan-2-ol, and ethanol, most likely because these molecules become too small to effectively stabilize the critical ice embryo. Overall, our results are consistent with PVA polymers and oligomers acting as heterogeneous ice nucleators.
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Affiliation(s)
- Lukas Eickhoff
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Mira Keßler
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Christopher Stubbs
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jakob Derksen
- Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Martina Viefhues
- Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Dario Anselmetti
- Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Berthold Hoge
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Thomas Koop
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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10
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Gomes PSFC, Gomes DEB, Bernardi RC. Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy. FRONTIERS IN BIOINFORMATICS 2022; 2:983306. [PMID: 36304287 PMCID: PMC9580946 DOI: 10.3389/fbinf.2022.983306] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Mechanoactive proteins are essential for a myriad of physiological and pathological processes. Guided by the advances in single-molecule force spectroscopy (SMFS), we have reached a molecular-level understanding of how mechanoactive proteins sense and respond to mechanical forces. However, even SMFS has its limitations, including the lack of detailed structural information during force-loading experiments. That is where molecular dynamics (MD) methods shine, bringing atomistic details with femtosecond time-resolution. However, MD heavily relies on the availability of high-resolution structural data, which is not available for most proteins. For instance, the Protein Data Bank currently has 192K structures deposited, against 231M protein sequences available on Uniprot. But many are betting that this gap might become much smaller soon. Over the past year, the AI-based AlphaFold created a buzz on the structural biology field by being able to predict near-native protein folds from their sequences. For some, AlphaFold is causing the merge of structural biology with bioinformatics. Here, using an in silico SMFS approach pioneered by our group, we investigate how reliable AlphaFold structure predictions are to investigate mechanical properties of Staphylococcus bacteria adhesins proteins. Our results show that AlphaFold produce extremally reliable protein folds, but in many cases is unable to predict high-resolution protein complexes accurately. Nonetheless, the results show that AlphaFold can revolutionize the investigation of these proteins, particularly by allowing high-throughput scanning of protein structures. Meanwhile, we show that the AlphaFold results need to be validated and should not be employed blindly, with the risk of obtaining an erroneous protein mechanism.
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