1
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Zhu Q, Nicolardi S, Wang Y, Liu Y, Xu P, Wang J, Zhu D, Yu B. Expeditious chemical synthesis of xylomannans disproves the proposed antifreeze activities. Natl Sci Rev 2024; 11:nwae296. [PMID: 39315280 PMCID: PMC11418650 DOI: 10.1093/nsr/nwae296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/23/2024] [Accepted: 08/01/2024] [Indexed: 09/25/2024] Open
Abstract
Cold-adapted species are able to generate cryoprotective proteins and glycoproteins to prevent freezing damage. The [→4)-β-D-Manp-(1→4)-β-D-Xylp-(1→] n xylomannan from the Alaska beetle Upis ceramboides was disclosed by Walters and co-workers in 2009 as the first glycan-based antifreeze agent, which was later reported to be found in diverse taxa. Here, we report the rapid synthesis of four types of xylomannans, including the proposed antifreeze xylomannan up to a 64-mer (Type I), the regioisomeric [→3)-β-D-Manp-(1→4)-β-D-Xylp-(1→] n 16-mer (Type II), the diastereomeric [→4)-β-L-Manp-(1→4)-β-D-Xylp-(1→] n 16-mer (Type III) and the block-wise [→4)-β-D-Manp-(1→] m [→4)-β-D-Xylp-(1→] n 32-mer (Type IV), by employing a strategic iterative exponential glycan growth (IEGG) process. The nuclear magnetic resonance spectral data of the alleged natural xylomannan are in accordance only to those of the block-wise Type IV glycan and none of these synthetic xylomannans has been found to be capable of inducing thermal hysteresis. These results disprove the previous reports about the natural occurrence of antifreeze xylomannans.
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Affiliation(s)
- Qian Zhu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, The Netherlands
| | - Yuanguang Wang
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yasong Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dapeng Zhu
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Biao Yu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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2
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Podbevšek D, Jung Y, Khan MK, Yu H, Tu RS, Chen X. The role of water mobility on water-responsive actuation of silk. Nat Commun 2024; 15:8287. [PMID: 39333569 PMCID: PMC11436739 DOI: 10.1038/s41467-024-52715-6] [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: 01/17/2024] [Accepted: 09/19/2024] [Indexed: 09/29/2024] Open
Abstract
Biological water-responsive materials that deform with changes in relative humidity have recently demonstrated record-high actuation energy densities, showing promise as high-performance actuators for various engineering applications. However, there is a lack of theories capable of explaining or predicting the stress generated during water-responsiveness. Here, we show that the nanoscale confinement of water dominates the macroscopic dehydration-induced stress of the regenerated silk fibroin. We modified silk fibroin's secondary structure, which leads to various distributions of bulk-like mobile and tightly bound water populations. Interestingly, despite these structure variations, all silk samples start to exert force when the bound-to-mobile (B/M) ratio of confined water reaches the same level. This critical B/M water ratio suggests a common threshold above which the chemical potential of water instigates the actuation. Our findings serve as guidelines for predicting and engineering silk's WR behavior and suggest the potential of describing the WR behavior of biopolymers through confined water.
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Affiliation(s)
- Darjan Podbevšek
- Advanced Science Research Center (ASRC) at the Graduate Center, The City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA
| | - Yeojin Jung
- Advanced Science Research Center (ASRC) at the Graduate Center, The City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA
| | - Maheen K Khan
- Advanced Science Research Center (ASRC) at the Graduate Center, The City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA
| | - Honghui Yu
- Department of Mechanical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA
| | - Raymond S Tu
- Advanced Science Research Center (ASRC) at the Graduate Center, The City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA.
| | - Xi Chen
- Advanced Science Research Center (ASRC) at the Graduate Center, The City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA.
- PhD Programs in Chemistry and Physics, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA.
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3
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Eskandari A, Leow TC, Rahman MBA, Oslan SN. Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024:10.1007/s00249-024-01719-7. [PMID: 39327310 DOI: 10.1007/s00249-024-01719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 06/18/2024] [Accepted: 07/02/2024] [Indexed: 09/28/2024]
Abstract
Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improve the cryopreservation activity of an AFPIV. In this in silico study, the helical peptide afp1m from an Antarctic yeast AFP was modeled into a sculpin AFPIV, to replace each of its four α-helices in turn, using various computational tools. Additionally, a new linker between the first two helices of AFPIV was designed, based on a flounder AFPI, to boost the ice interaction activity of the mutants. Bioinformatics tools such as ExPASy Prot-Param, Pep-Wheel, SOPMA, GOR IV, Swiss-Model, Phyre2, MODFOLD, MolPropity, and ProQ were used to validate and analyze the structural and functional properties of the model proteins. Furthermore, to evaluate the AFP/ice interaction, molecular dynamics (MD) simulations were executed for 20, 100, and 500 ns at various temperatures using GROMACS software. The primary, secondary, and 3D modeling analysis showed the best model for a redesigned antifreeze protein (AFP1mb, with afp1m in place of the fourth AFPIV helix) with a QMEAN (Swiss-Model) Z score value of 0.36, a confidence of 99.5%, a coverage score of 22%, and a p value of 0.01. The results of the MD simulations illustrated that AFP1mb had more rigidity and better ice interactions as a potential cryoprotectant than the other models; it also displayed enhanced activity in limiting ice growth at different temperatures.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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4
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Maiti A, Erimban S, Daschakraborty S. Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments. Chem Commun (Camb) 2024; 60:10280-10294. [PMID: 39190300 DOI: 10.1039/d4cc03114h] [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: 08/28/2024]
Abstract
The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India.
| | - Shakkira Erimban
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India.
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5
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Graham LA, Davies PL. Fish antifreeze protein origin in sculpins by frameshifting within a duplicated housekeeping gene. FEBS J 2024; 291:4043-4061. [PMID: 38923815 DOI: 10.1111/febs.17205] [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: 11/13/2023] [Revised: 03/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Antifreeze proteins (AFPs) are found in a variety of marine cold-water fishes where they prevent freezing by binding to nascent ice crystals. Their diversity (types I, II, III and antifreeze glycoproteins), as well as their scattered taxonomic distribution hint at their complex evolutionary history. In particular, type I AFPs appear to have arisen in response to the Late Cenozoic Ice Age that began ~ 34 million years ago via convergence in four different groups of fish that diverged from lineages lacking this AFP. The progenitor of the alanine-rich α-helical type I AFPs of sculpins has now been identified as lunapark, an integral membrane protein of the endoplasmic reticulum. Following gene duplication and loss of all but three of the 15 exons, the final exon, which encoded a glutamate- and glutamine-rich segment, was converted to an alanine-rich sequence by a combination of frameshifting and mutation. Subsequent gene duplications produced numerous isoforms falling into four distinct groups. The origin of the flounder type I AFP is quite different. Here, a small segment from the original antiviral protein gene was amplified and the rest of the coding sequence was lost, while the gene structure was largely retained. The independent origins of type I AFPs with up to 83% sequence identity in flounder and sculpin demonstrate strong convergent selection at the level of protein sequence for alanine-rich single alpha helices that bind to ice. Recent acquisition of these AFPs has allowed sculpins to occupy icy seawater niches with reduced competition and predation from other teleost species.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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6
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Ryan M, Gao L, Valiyaveetil FI, Kananenka AA, Zanni MT. Water inside the Selectivity Filter of a K + Ion Channel: Structural Heterogeneity, Picosecond Dynamics, and Hydrogen Bonding. J Am Chem Soc 2024; 146:1543-1553. [PMID: 38181505 PMCID: PMC10797622 DOI: 10.1021/jacs.3c11513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Water inside biological ion channels regulates the key properties of these proteins, such as selectivity, ion conductance, and gating. In this article, we measure the picosecond spectral diffusion of amide I vibrations of an isotope-labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100-2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope-labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D line shapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent or nonadjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations was observed on a picosecond timescale. These dynamics are in stark contrast with liquid water, which remains highly dynamic even in the presence of ions at high concentrations.
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Affiliation(s)
- Matthew
J. Ryan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lujia Gao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Francis I. Valiyaveetil
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Alexei A. Kananenka
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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7
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Drori R, Stevens CA. Divergent Mechanisms of Ice Growth Inhibition by Antifreeze Proteins. Methods Mol Biol 2024; 2730:169-181. [PMID: 37943458 DOI: 10.1007/978-1-0716-3503-2_12] [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
Antifreeze proteins (AFPs) are biomolecules that can bind to ice and hinder its growth, thus holding significant potential for biotechnological and biomedical applications. AFPs are a subset of ice-binding proteins (IBPs) and are found in various organisms across different life kingdoms. This mini-review investigates the underlying mechanisms by which AFPs impede ice growth, emphasizing the disparities between hyperactive and moderate AFPs. Hyperactive AFPs exhibit heightened thermal hysteresis (TH) activity and can bind to both the basal and prism planes of ice crystals, enabling them to endure extremely cold temperatures. In contrast, moderate AFPs predominantly bind to the prism/pyramidal planes and demonstrate lower TH activity. The structural diversity of AFPs and the presence of ordered water molecules on their ice-binding sites (IBS) have been subjects of debate among researchers. Multiple hypotheses have been proposed concerning the significance of ordered water molecules in ice binding. Gaining insights into the binding dynamics and the factors influencing TH activity in AFPs is crucial for the development of efficient synthetic compounds and the establishment of comprehensive models to elucidate ice growth inhibition. Here we emphasize the necessity for further research to unravel the mechanisms of AFPs and presents a pathway for constructing models capable of comprehensively explaining their inhibitory effects on ice growth.
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Affiliation(s)
- Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, NY, USA.
| | - Corey A Stevens
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Vance TDR. Ice Isn't the Only Crystal in Town: Structure Determination of Ice-Binding Proteins via X-Ray Crystallography. Methods Mol Biol 2024; 2730:35-62. [PMID: 37943449 DOI: 10.1007/978-1-0716-3503-2_3] [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 proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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9
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Ryan MJ, Gao L, Valiyaveetil FI, Kananenka AA, Zanni MT. Water inside the selectivity filter of a K + ion channel: structural heterogeneity, picosecond dynamics, and hydrogen-bonding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567415. [PMID: 38014355 PMCID: PMC10680850 DOI: 10.1101/2023.11.16.567415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Water inside biological ion channels regulates the key properties of these proteins such as selectivity, ion conductance, and gating. In this Article we measure the picosecond spectral diffusion of amide I vibrations of an isotope labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100 - 2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D lineshapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent, or non-adjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations were observed on a picosecond timescale. These dynamics are in stark contrast with liquid water that remains highly dynamic even in the presence of ions at high concentrations.
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Affiliation(s)
- Matthew J. Ryan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lujia Gao
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Francis I. Valiyaveetil
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexei A. Kananenka
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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10
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Ramón A, Esteves A, Villadóniga C, Chalar C, Castro-Sowinski S. A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies. Braz J Microbiol 2023; 54:2259-2287. [PMID: 37477802 PMCID: PMC10484896 DOI: 10.1007/s42770-023-01057-4] [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: 03/20/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000 m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Adriana Esteves
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Carolina Villadóniga
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Cora Chalar
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
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11
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Huard DJE, Johnson AM, Fan Z, Kenney LG, Xu M, Drori R, Gumbart JC, Dai S, Lieberman RL, Glass JB. Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein. PNAS NEXUS 2023; 2:pgad268. [PMID: 37644917 PMCID: PMC10462418 DOI: 10.1093/pnasnexus/pgad268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023]
Abstract
Methane clathrates on continental margins contain the largest stores of hydrocarbons on Earth, yet the role of biomolecules in clathrate formation and stability remains almost completely unknown. Here, we report new methane clathrate-binding proteins (CbpAs) of bacterial origin discovered in metagenomes from gas clathrate-bearing ocean sediments. CbpAs show similar suppression of methane clathrate growth as the commercial gas clathrate inhibitor polyvinylpyrrolidone and inhibit clathrate growth at lower concentrations than antifreeze proteins (AFPs) previously tested. Unlike AFPs, CbpAs are selective for clathrate over ice. CbpA3 adopts a nonglobular, extended structure with an exposed hydrophobic surface, and, unexpectedly, its TxxxAxxxAxx motif common to AFPs is buried and not involved in clathrate binding. Instead, simulations and mutagenesis suggest a bipartite interaction of CbpAs with methane clathrate, with the pyrrolidine ring of a highly conserved proline residue mediating binding by filling empty clathrate cages. The discovery that CbpAs exert such potent control on methane clathrate properties implies that biomolecules from native sediment bacteria may be important for clathrate stability and habitability.
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Affiliation(s)
- Dustin J E Huard
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Abigail M Johnson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, 315 Ferst Dr NW, Atlanta, GA 30332, USA
| | - Lydia G Kenney
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Manlin Xu
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Ave Room 548, New York, NY 10016, USA
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Sheng Dai
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 790 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
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12
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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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13
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Lin B, Jiang J, Zeng XC, Li L. Temperature-pressure phase diagram of confined monolayer water/ice at first-principles accuracy with a machine-learning force field. Nat Commun 2023; 14:4110. [PMID: 37433823 DOI: 10.1038/s41467-023-39829-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Understanding the phase behaviour of nanoconfined water films is of fundamental importance in broad fields of science and engineering. However, the phase behaviour of the thinnest water film - monolayer water - is still incompletely known. Here, we developed a machine-learning force field (MLFF) at first-principles accuracy to determine the phase diagram of monolayer water/ice in nanoconfinement with hydrophobic walls. We observed the spontaneous formation of two previously unreported high-density ices, namely, zigzag quasi-bilayer ice (ZZ-qBI) and branched-zigzag quasi-bilayer ice (bZZ-qBI). Unlike conventional bilayer ices, few inter-layer hydrogen bonds were observed in both quasi-bilayer ices. Notably, the bZZ-qBI entails a unique hydrogen-bonding network that consists of two distinctive types of hydrogen bonds. Moreover, we identified, for the first time, the stable region for the lowest-density [Formula: see text] monolayer ice (LD-48MI) at negative pressures (<-0.3 GPa). Overall, the MLFF enables large-scale first-principle-level molecular dynamics (MD) simulations of the spontaneous transition from the liquid water to a plethora of monolayer ices, including hexagonal, pentagonal, square, zigzag (ZZMI), and hexatic monolayer ices. These findings will enrich our understanding of the phase behaviour of the nanoconfined water/ices and provide a guide for future experimental realization of the 2D ices.
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Affiliation(s)
- Bo Lin
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Jian Jiang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, 999077, Hong Kong
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Xiao Cheng Zeng
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, 999077, Hong Kong.
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Lei Li
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
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14
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Dong X, Liu Z, Wei J, Zheng G, Li H, Wang Y, Tian H, Cui J, Wu Z, Cao X, Xu C. The BrAFP1 promoter drives gene-specific expression in leaves and stems of winter rapeseed (Brassica rapa L.) under cold induction. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111669. [PMID: 36870371 DOI: 10.1016/j.plantsci.2023.111669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
BrAFP1(antifreeze protein in winter turnip rape) effectively limits recrystallization and growth of ice crystals. The BrAFP1 expression level determines whether the freezing-induced damage to winter turnip rape plants is avoided. This study analyzed the activity of the BrAFP1 promoters of several varieties at various cold tolerance levels. We cloned the BrAFP1 promoters from five winter rapeseed cultivars. The multiple sequence alignment revealed the presence of one inDel and eight single-nucleotide mutations (SNMs) in the promoters. One of these SNMs (base mutation from C to T) at the -836 site away from the transcription start site (TSS) enhanced the transcriptional activity of the promoter at low temperature. The promoter activity was specific in cotyledons and hypocotyls during the seedling stage and was referential in stems, leaves, and flowers but not the calyx. This consequently drove the downstream gene to be specifically expressed in leaves and stems, but not in roots at low temperature. The truncated fragment GUS staining assays revealed that the core region of the BrAFP1 promoter was included in the 98 bp fragment from the -933 to -836 site away from the TSS, which was necessary for transcriptional activity. The LTR element of the promoter significantly enhanced expression at low temperatures and suppressed expression at moderate temperatures. Moreover, the BrAFP1 5'-UTR intron bound the scarecrow-like transcription factor and enhanced expression at low temperature.
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Affiliation(s)
- Xiaoyun Dong
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zigang Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiaping Wei
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoqiang Zheng
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Hui Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ying Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Haiyan Tian
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junmei Cui
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zefeng Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaodong Cao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunmei Xu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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15
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Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean. Genes (Basel) 2023; 14:genes14020363. [PMID: 36833289 PMCID: PMC9957290 DOI: 10.3390/genes14020363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.
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16
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Samuel AZ, Sugiyama K, Takeyama H. Direct intracellular detection of biomolecule specific bound-water with Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121870. [PMID: 36116410 DOI: 10.1016/j.saa.2022.121870] [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: 06/02/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Lipids, proteins, and nucleic acids have closely associated water molecules (Bound water), which exhibit considerably different physical properties compared to bulk water. Here we investigate the possibility of resolving Raman spectra of the specific hydration shell of these biomolecules in intracellular regions using Raman imaging. Lipids and proteins + nucleic acids Raman spectral components resolved in the analysis showed associated water spectral features, which are uniquely different from that of bulk water. These spectral profiles agree with water spectral profile observed in the case of corresponding hydrated pure biomolecules. The results show the prospects of Raman imaging in examining intracellular hydration in biomolecules and its functional relation.
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Affiliation(s)
- Ashok Zachariah Samuel
- Research Organization for Nano and Life Innovations, Waseda University, 513, Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan.
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovations, Waseda University, 513, Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Japan, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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17
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Graham LA, Gauthier SY, Davies PL. Origin of an antifreeze protein gene in response to Cenozoic climate change. Sci Rep 2022; 12:8536. [PMID: 35595816 PMCID: PMC9122973 DOI: 10.1038/s41598-022-12446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth within fish and protect them from freezing in icy seawater. Alanine-rich, alpha-helical AFPs (type I) have independently (convergently) evolved in four branches of fishes, one of which is a subsection of the righteye flounders. The origin of this gene family has been elucidated by sequencing two loci from a starry flounder, Platichthys stellatus, collected off Vancouver Island, British Columbia. The first locus had two alleles that demonstrated the plasticity of the AFP gene family, one encoding 33 AFPs and the other allele only four. In the closely related Pacific halibut, this locus encodes multiple Gig2 (antiviral) proteins, but in the starry flounder, the Gig2 genes were found at a second locus due to a lineage-specific duplication event. An ancestral Gig2 gave rise to a 3-kDa "skin" AFP isoform, encoding three Ala-rich 11-a.a. repeats, that is expressed in skin and other peripheral tissues. Subsequent gene duplications, followed by internal duplications of the 11 a.a. repeat and the gain of a signal sequence, gave rise to circulating AFP isoforms. One of these, the "hyperactive" 32-kDa Maxi likely underwent a contraction to a shorter 3.3-kDa "liver" isoform. Present day starry flounders found in Pacific Rim coastal waters from California to Alaska show a positive correlation between latitude and AFP gene dosage, with the shorter allele being more prevalent at lower latitudes. This study conclusively demonstrates that the flounder AFP arose from the Gig2 gene, so it is evolutionarily unrelated to the three other classes of type I AFPs from non-flounders. Additionally, this gene arose and underwent amplification coincident with the onset of ocean cooling during the Cenozoic ice ages.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Sherry Y Gauthier
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
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18
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Kim BI, Boehm RD, Agrusa H. Coil-to-Bridge Transitions of Self-Assembled Water Chains Observed in a Nanoscopic Meniscus. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:4538-4546. [PMID: 35394791 PMCID: PMC9022434 DOI: 10.1021/acs.langmuir.1c03100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Ten downward portions in the large oscillatory force-distance curve reported earlier are analyzed to understand a nanoscale water meniscus confined between a sharp probe and a flat substrate in air. The sigmoidal shape of each portion leads to the assumption that the meniscus is made up of n independent transitions of two states: one for a coil state and the other for a bridge state. The analysis reveals that each downward portion occurs due to a coil-to-bridge transition of n self-assembled water chains whose length ranges between 197 and 383 chain units. The transition provides novel insights into water's unique properties like high surface tension and the long-range condensation distances.
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19
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Xie X, Wu P, Huang X, Bai W, Li B, Shi N. Retro-protein XXA is a remarkable solubilizing fusion tag for inclusion bodies. Microb Cell Fact 2022; 21:51. [PMID: 35366873 PMCID: PMC8977028 DOI: 10.1186/s12934-022-01776-7] [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: 12/03/2021] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background Producing large amounts of soluble proteins from bacteria remains a challenge, despite the help of current various solubilizing fusion tags. Thus, developing novel tags is necessary. Antifreeze protein (AFP) has excellent solubility and hydrophilicity, but there are no current reports on its use as a solubilizing fusion tag. Additionally, there is no precedent for using retro-proteins (reverse sequence) as solubilizing fusion tags. Therefore, we selected the antifreeze protein AXX and obtained its retro-protein XXA by synthesizing the XXA gene for the development of a new solubilizing fusion tag. Results XXA exhibits better stability and ease of expression than AXX; hence, we focused the development of the solubilizing fusion tag on XXA. XXA fused with the tested inclusion bodies, significantly increasing the soluble expression compared with commonly used solubilizing fusion tags such as GST, Trx, Sumo, MBP, and NusA. The tested proteins became soluble after fusion with the XXA tag, and they could be purified. They maintained a soluble form after XXA tag removal. Finally, we used enzymatic digestion reaction and western blot experiments to verify that bdNEDP1 and NbALFA, which were soluble expressed by fusion with XXA, were active. Conclusion We developed the novel solubilizing fusion tag XXA, which could more effectively facilitate the soluble expression of inclusion bodies compared with current commonly used tags. XXA could function at both low and high temperatures, and its moderate molecular weight has a limited impact on the output. These properties make XXA an ideal fusion tag for future research and industrial production. Moreover, for the first time, we highlighted the broad potential of antifreeze protein as a solubilizing fusion tag, bringing retro-protein into practical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01776-7.
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Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 2022; 126:1212-1231. [PMID: 35128921 PMCID: PMC9281400 DOI: 10.1021/acs.jpcb.1c10750] [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] [Indexed: 11/28/2022]
Abstract
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
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Affiliation(s)
- Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jack B Maguire
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shirley Yuen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jermel Griffin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward A Esposito
- Malvern Panalytical Inc, Northhampton, Massachsetts 01060, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 08544, United States
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center, Stanford University, Menlo Park, California 94025, United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Materials Design and Innovation, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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21
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Gharib G, Saeidiharzand S, Sadaghiani AK, Koşar A. Antifreeze Proteins: A Tale of Evolution From Origin to Energy Applications. Front Bioeng Biotechnol 2022; 9:770588. [PMID: 35186912 PMCID: PMC8851421 DOI: 10.3389/fbioe.2021.770588] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/31/2021] [Indexed: 11/19/2022] Open
Abstract
Icing and formation of ice crystals is a major obstacle against applications ranging from energy systems to transportation and aviation. Icing not only introduces excess thermal resistance, but it also reduces the safety in operating systems. Many organisms living under harsh climate and subzero temperature conditions have developed extraordinary survival strategies to avoid or delay ice crystal formation. There are several types of antifreeze glycoproteins with ice-binding ability to hamper ice growth, ice nucleation, and recrystallization. Scientists adopted similar approaches to utilize a new generation of engineered antifreeze and ice-binding proteins as bio cryoprotective agents for preservation and industrial applications. There are numerous types of antifreeze proteins (AFPs) categorized according to their structures and functions. The main challenge in employing such biomolecules on industrial surfaces is the stabilization/coating with high efficiency. In this review, we discuss various classes of antifreeze proteins. Our particular focus is on the elaboration of potential industrial applications of anti-freeze polypeptides.
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Affiliation(s)
- Ghazaleh Gharib
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
| | - Shaghayegh Saeidiharzand
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
| | - Abdolali K. Sadaghiani
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- *Correspondence: Abdolali K. Sadaghiani, ; Ali Koşar,
| | - Ali Koşar
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- *Correspondence: Abdolali K. Sadaghiani, ; Ali Koşar,
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22
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Jin T, Long F, Zhang Q, Zhuang W. Site-Specific Water Dynamics in the First Hydration Layer of an Anti-Freeze Glyco-Protein: A Simulation Study. Phys Chem Chem Phys 2022; 24:21165-21177. [DOI: 10.1039/d2cp00883a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antifreeze glycoproteins (AFGPs) inhibit ice recrystallization by a mechanism remaining largely elusive. Dynamics of AFGPs’ hydration water and its involvement in the antifreeze activity, for instance, have not been identified...
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23
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Gore M, Narvekar A, Bhagwat A, Jain R, Dandekar P. Macromolecular cryoprotectants for the preservation of mammalian cell culture: lessons from crowding, overview and perspectives. J Mater Chem B 2021; 10:143-169. [PMID: 34913462 DOI: 10.1039/d1tb01449h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cryopreservation is a process used for the storage of mammalian cells at a very low temperature, in a state of 'suspended animation.' Highly effective and safe macromolecular cryoprotectants (CPAs) have gained significant attention as they obviate the toxicity of conventional CPAs like dimethyl sulfoxide (DMSO) and reduce the risks involved in the storage of cultures at liquid nitrogen temperatures. These agents provide cryoprotection through multiple mechanisms, involving extracellular and intracellular macromolecular crowding, thereby impacting the biophysical and biochemical dynamics of the freezing medium and the cryopreserved cells. These CPAs vary in their structures and physicochemical properties, which influence their cryoprotective activities. Moreover, the introduction of polymeric crowders in the cryopreservation media enables serum-free storage at low-DMSO concentrations and high-temperature vitrification of frozen cultures (-80 °C). This review highlights the need for macromolecular CPAs and describes their mechanisms of cryopreservation, by elucidating the role of crowding effects. It also classifies the macromolecules based on their chemistry and their structure-activity relationships. Furthermore, this article provides perspectives on the factors that may influence the outcomes of the cell freezing process or may help in designing and evaluating prospective macromolecules. This manuscript also includes case studies about cellular investigations that have been conducted to demonstrate the cryoprotective potential of macromolecular CPAs. Ultimately, this review provides essential directives that will further improve the cell cryopreservation process and may encourage the use of macromolecular CPAs to fortify basic, applied, and translational research.
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Affiliation(s)
- Manish Gore
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Aditya Narvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Advait Bhagwat
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
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24
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Wu X, Yao F, Zhang H, Li J. Antifreeze proteins and their biomimetics for cell cryopreservation: Mechanism, function and application-A review. Int J Biol Macromol 2021; 192:1276-1291. [PMID: 34634336 DOI: 10.1016/j.ijbiomac.2021.09.211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Cell-based therapy is a promising technology for intractable diseases and health care applications, in which cryopreservation has become an essential procedure to realize the production of therapeutic cells. Ice recrystallization is the major factor that affects the post-thaw viability of cells. As a typical series of biomacromolecules with ice recrystallization inhibition (IRI) activity, antifreeze proteins (AFPs) have been employed in cell cryopreservation. Meanwhile, synthesized materials with IRI activity have emerged in the name of biomimetics of AFPs to expand their availability and practicality. However, fabrication of AFPs mimetics is in a chaotic period. There remains little commonality among different AFPs mimetics, then it is difficult to set guidelines on their design. With no doubt, a comprehensive understanding on the antifreezing mechanism of AFPs in molecular level will enable us to rebuild the function of AFPs, and provide convenience to clarify the relationship between structure and function of these early stage biomimetics. In this review, we would discuss those previously reported biomimetics to summarize their structure characteristics concerning the IRI activity and attempt to develop a roadmap for guiding the design of novel AFPs mimetics.
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Affiliation(s)
- Xiaojun Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Fanglian Yao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Hong Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Junjie Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China.
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25
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Soussana TN, Weissman H, Rybtchinski B, Drori R. Adsorption-Inhibition of Clathrate Hydrates by Self-Assembled Nanostructures. Chemphyschem 2021; 22:2182-2189. [PMID: 34407283 DOI: 10.1002/cphc.202100463] [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: 06/15/2021] [Revised: 08/11/2021] [Indexed: 11/11/2022]
Abstract
The mechanism by which safranine O (SFO), an ice growth inhibitor, halts the growth of single crystal tetrahydrofuran (THF) clathrate hydrates was explored using microfluidics coupled with cold stages and fluorescence microscopy. THF hydrates grown in SFO solutions exhibited morphology changes and were shaped as truncated octahedrons or hexagons. Fluorescence microscopy and microfluidics demonstrated that SFO binds to the surface of THF hydrates on specific crystal planes. Cryo-TEM experiments of aqueous solutions containing millimolar concentrations of SFO exhibited the formation of bilayered lamellae with an average thickness of 4.2±0.2 nm covering several μm2 . Altogether, these results indicate that SFO forms supramolecular lamellae in solution, which might bind to the surface of the hydrate and inhibit further growth. As an ice and hydrate inhibitor, SFO may bind to the surface of these crystals via ordered water molecules near its amine and methyl groups, similar to some antifreeze proteins.
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Affiliation(s)
- Tamar Nicole Soussana
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
| | - Haim Weissman
- Department of Organic Chemistry, Weizmann Institute of Science, 234 Hertzel Street, PO Box 26, Rehovot, 7610001, Israel
| | - Boris Rybtchinski
- Department of Organic Chemistry, Weizmann Institute of Science, 234 Hertzel Street, PO Box 26, Rehovot, 7610001, Israel
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
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26
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Wang F, Zhuo Y, He Z, Xiao S, He J, Zhang Z. Dynamic Anti-Icing Surfaces (DAIS). ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101163. [PMID: 34499428 PMCID: PMC8564445 DOI: 10.1002/advs.202101163] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/24/2021] [Indexed: 05/03/2023]
Abstract
Remarkable progress has been made in surface icephobicity in the recent years. The mainstream standpoint of the reported antiicing surfaces yet only considers the ice-substrate interface and its adjacent regions being of static nature. In reality, the local structures and the overall properties of ice-substrate interfaces evolve with time, temperature and various external stimuli. Understanding the dynamic properties of the icing interface is crucial for shedding new light on the design of new anti-icing surfaces to meet challenges of harsh conditions including extremely low temperature and/or long working time. This article surveys the state-of-the-art anti-icing surfaces and dissects their dynamic changes of the chemical/physical states at icing interface. According to the focused critical ice-substrate contacting locations, namely the most important ice-substrate interface and the adjacent regions in the substrate and in the ice, the available anti-icing surfaces are for the first time re-assessed by taking the dynamic evolution into account. Subsequently, the recent works in the preparation of dynamic anti-icing surfaces (DAIS) that consider time-evolving properties, with their potentials in practical applications, and the challenges confronted are summarized and discussed, aiming for providing a thorough review of the promising concept of DAIS for guiding the future icephobic materials designs.
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Affiliation(s)
- Feng Wang
- NTNU Nanomechanical LabDepartment of Structural EngineeringNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
| | - Yizhi Zhuo
- NTNU Nanomechanical LabDepartment of Structural EngineeringNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
| | - Zhiwei He
- College of Materials and Environmental EngineeringHangzhou Dianzi UniversityHangzhou310018China
| | - Senbo Xiao
- NTNU Nanomechanical LabDepartment of Structural EngineeringNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
| | - Jianying He
- NTNU Nanomechanical LabDepartment of Structural EngineeringNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
| | - Zhiliang Zhang
- NTNU Nanomechanical LabDepartment of Structural EngineeringNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
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Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
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Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
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28
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Parui S, Jana B. Cold denaturation induced helix-to-helix transition and its implication to activity of helical antifreeze protein. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Pal P, Chakraborty S, Jana B. Differential Hydration of Ice‐Binding Surface of Globular and Hyperactive Antifreeze Proteins. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Prasun Pal
- School of Chemical Sciences Indian Association for the Cultivation of Science, Jadavpur Kolkata 700032 India
| | | | - Biman Jana
- School of Chemical Sciences Indian Association for the Cultivation of Science, Jadavpur Kolkata 700032 India
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Georgiou P, Marton HL, Baker AN, Congdon TR, Whale TF, Gibson MI. Polymer Self-Assembly Induced Enhancement of Ice Recrystallization Inhibition. J Am Chem Soc 2021; 143:7449-7461. [PMID: 33944551 PMCID: PMC8154521 DOI: 10.1021/jacs.1c01963] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Indexed: 02/07/2023]
Abstract
Ice binding proteins modulate ice nucleation/growth and have huge (bio)technological potential. There are few synthetic materials that reproduce their function, and rational design is challenging due to the outstanding questions about the mechanisms of ice binding, including whether ice binding is essential to reproduce all their macroscopic properties. Here we report that nanoparticles obtained by polymerization-induced self-assembly (PISA) inhibit ice recrystallization (IRI) despite their constituent polymers having no apparent activity. Poly(ethylene glycol), poly(dimethylacrylamide), and poly(vinylpyrrolidone) coronas were all IRI-active when assembled into nanoparticles. Different core-forming blocks were also screened, revealing the core chemistry had no effect. These observations show ice binding domains are not essential for macroscopic IRI activity and suggest that the size, and crowding, of polymers may increase the IRI activity of "non-active" polymers. It was also discovered that poly(vinylpyrrolidone) particles had ice crystal shaping activity, indicating this polymer can engage ice crystal surfaces, even though on its own it does not show any appreciable ice recrystallization inhibition. Larger (vesicle) nanoparticles are shown to have higher ice recrystallization inhibition activity compared to smaller (sphere) particles, whereas ice nucleation activity was not found for any material. This shows that assembly into larger structures can increase IRI activity and that increasing the "size" of an IRI does not always lead to ice nucleation. This nanoparticle approach offers a platform toward ice-controlling soft materials and insight into how IRI activity scales with molecular size of additives.
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Affiliation(s)
- Panagiotis
G. Georgiou
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
| | - Huba L. Marton
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
| | - Alexander N. Baker
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
| | - Thomas R. Congdon
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
| | - Thomas F. Whale
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
- Warwick
Medical School, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
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32
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Characterization of the Features of Water Inside the SecY Translocon. J Membr Biol 2021; 254:133-139. [PMID: 33811496 DOI: 10.1007/s00232-021-00178-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Despite extended experimental and computational studies, the mechanism regulating membrane protein folding and stability in cell membranes is not fully understood. In this review, I will provide a personal and partial account of the scientific efforts undertaken by Dr. Stephen White to shed light on this topic. After briefly describing the role of water and the hydrophobic effect on cellular processes, I will discuss the physical chemistry of water confined inside the SecY translocon pore. I conclude with a review of recent literature that attempts to answer fundamental questions on the pathway and energetics of translocon-guided membrane protein insertion.
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33
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Khan NMMU, Arai T, Tsuda S, Kondo H. Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. Sci Rep 2021; 11:5971. [PMID: 33727595 PMCID: PMC7966756 DOI: 10.1038/s41598-021-85559-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth by adsorbing onto specific ice planes. Microbial AFPs show diverse antifreeze activity and ice plane specificity, while sharing a common molecular scaffold. To probe the molecular mechanisms responsible for AFP activity, we here characterized the antifreeze activity and crystal structure of TisAFP7 from the snow mold fungus Typhula ishikariensis. TisAFP7 exhibited intermediate activity, with the ability to bind the basal plane, compared with a hyperactive isoform TisAFP8 and a moderately active isoform TisAFP6. Analysis of the TisAFP7 crystal structure revealed a bound-water network arranged in a zigzag pattern on the surface of the protein's ice-binding site (IBS). While the three AFP isoforms shared the water network pattern, the network on TisAFP7 IBS was not extensive, which was likely related to its intermediate activity. Analysis of the TisAFP7 crystal structure also revealed the presence of additional water molecules that form a ring-like network surrounding the hydrophobic side chain of a crucial IBS phenylalanine, which might be responsible for the increased adsorption of AFP molecule onto the basal plane. Based on these observations, we propose that the extended water network and hydrophobic hydration at IBS together determine the TisAFP activity.
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Affiliation(s)
- N M-Mofiz Uddin Khan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Department of Chemistry, Dhaka University of Engineering and Technology, Gazipur Gazipur, 1700, Bangladesh
| | - Tatsuya Arai
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sakae Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.,OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8563, Japan
| | - Hidemasa Kondo
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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34
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Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface. Biochem J 2021; 477:3271-3286. [PMID: 32794579 DOI: 10.1042/bcj20200539] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 11/17/2022]
Abstract
Antifreeze proteins (AFPs) are characterized by their ability to adsorb to the surface of ice crystals and prevent any further crystal growth. AFPs have independently evolved for this purpose in a variety of organisms that encounter the threat of freezing, including many species of polar fish, insects, plants and microorganisms. Despite their diverse origins and structures, it has been suggested that all AFPs can organize ice-like water patterns on one side of the protein (the ice-binding site) that helps bind the AFP to ice. Here, to test this hypothesis, we have solved the crystal structure at 2.05 Å resolution of an AFP from the longhorn beetle, Rhagium mordax with five molecules in the unit cell. This AFP is hyperactive, and its crystal structure resembles that of the R. inquisitor ortholog in having a β-solenoid fold with a wide, flat ice-binding surface formed by four parallel rows of mainly Thr residues. The key difference between these structures is that the R. inquisitor AFP crystallized with its ice-binding site (IBS) making protein-protein contacts that limited the surface water patterns. Whereas the R. mordax AFP crystallized with the IBSs exposed to solvent enabling two layers of unrestricted ordered surface waters to be seen. These crystal waters make close matches to ice lattice waters on the basal and primary prism planes.
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35
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Kozuch DJ, Stillinger FH, Debenedetti PG. Genetic Algorithm Approach for the Optimization of Protein Antifreeze Activity Using Molecular Simulations. J Chem Theory Comput 2020; 16:7866-7873. [PMID: 33201707 DOI: 10.1021/acs.jctc.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antifreeze proteins (AFPs) are of much interest for their ability to inhibit ice growth at low concentrations. In this work, we present a genetic algorithm for the in silico design of AFP mutants with improved antifreeze activity, measured as the predicted thermal hysteresis at a fixed concentration, ΔTC. Central to the algorithm is our recently developed neural network method for predicting ΔTC from molecular simulations [Kozuch et al., PNAS, 115, 13252 (2018)]. Applying the algorithm to three structurally diverse AFPs, wfAFP, rQAE, and RiAFP, we find that significantly improved mutants are discovered for rQAE and RiAFP. Testing of the optimized mutants shows an increase in ΔTC of 0.572 ± 0.11 K (262 ± 50.6%) and 1.33 ± 0.14 K (39.9 ± 4.19%) over the native structures for rQAE and RiAFP, respectively. Structural analysis of the optimized mutants reveals that the algorithm is able to exploit two pathways for enhancing the predicted antifreeze activity of the mutants: (1) increasing the local order of surface waters by encouraging the formation of internal water channels in the protein and (2) increasing the total ice-binding area by improving the planar structure of the ice-binding surface. Additionally, analysis of all mutants explored by the algorithm reveals that a subset of residues, mainly nonpolar, are particularly helpful in improving antifreeze activity at the ice-binding surface.
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Affiliation(s)
- Daniel J Kozuch
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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36
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Johnson AM, Huard DJE, Kim J, Raut P, Dai S, Lieberman RL, Glass JB. Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure. CRYSTAL GROWTH & DESIGN 2020; 20:6290-6295. [PMID: 33414686 PMCID: PMC7786625 DOI: 10.1021/acs.cgd.0c00855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed. Type I Antifreeze Proteins (AFPs) from cold-water fish have been shown to bind to gas clathrates via repeating motifs of threonine and alanine. We tested whether proteins encoded in the genomes of bacteria native to natural gas clathrates bind to and alter clathrate morphology. We identified putative clathrate-binding proteins (CBPs) with multiple threonine/alanine motifs in a putative operon (cbp) in metagenomes from natural clathrate deposits. We recombinantly expressed and purified five CbpA proteins, four of which were stable, and experimentally confirmed that CbpAs bound to tetrahydrofuran (THF) clathrate, a low-pressure analogue for structure II gas clathrate. When grown in the presence of CbpAs, the THF clathrate was polycrystalline and platelike instead of forming single, octahedral crystals. Two CbpAs yielded branching clathrate crystals, similar to the effect of Type I AFP, while the other two produced hexagonal crystals parallel to the [1 1 1] plane, suggesting two distinct binding modes. Bacterial CBPs may find future utility in industry, such as maintaining a platelike structure during gas clathrate transportation.
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Affiliation(s)
- Abigail M Johnson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
| | - Dustin J E Huard
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
| | - Jongchan Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
| | - Priyam Raut
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
| | - Sheng Dai
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30324, United States
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37
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Zhang Y, Hu W, Sun J, Li Y, Chen C. Hydrogen bonds and hydrate interaction between RiAFP and water revealed by molecular dynamics simulations. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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38
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Dong X, Liu Z, Mi W, Xu C, Xu M, Zhou Y, Zhen G, Cao X, Fang X, Mi C. Overexpression of BrAFP1 gene from winter rapeseed (Brassica rapa) confers cold tolerance in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:338-345. [PMID: 32798902 DOI: 10.1016/j.plaphy.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Antifreeze proteins (AFPs) can bind to ice crystals and restrain the formation of larger crystals, a strategy vital to the survival of plants in freezing environments. The BrAFP1 from winter rapeseed cultivars 'Longyou 7' with high cold tolerance was cloned and overexpressed in Arabidopsis. BrAFP1 was localized in the cytoplasm and nucleus. Under cold stress, SOD activity and free proline content were higher, MDA content and relative conductivity were lower in transgenic lines than those in wide-type Arabidopsis. Frostbite of transgenic plants was minimized, whereas frostbite of the Arabidopsis afp1 mutant was severe. Transition of the amino acid at position 17 of BrAFP1 was related to the increased winter survival of the rapeseed cultivar. Cultivars with higher survival rates had a predilection for tyrosine, not tryptophan, at the 17th site in the amino sequence of BrAFP1. Transcription of BrAFP1 was induced more rapidly, and the expression of the gene was also higher, in Longyou 7 than that in Tianyou 4 under cold stress. Overall, the high expression of BrAPF1 confers more cold-tolerance in Longyou 7.
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Affiliation(s)
- Xiaoyun Dong
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zigang Liu
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Wenbo Mi
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chunmei Xu
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Minxia Xu
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ya Zhou
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Guoqiang Zhen
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaodong Cao
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xinlin Fang
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chao Mi
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
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Xiang L, Zhang P, Liu C, He X, Li HB, Li Y, Wang Z, Hihath J, Kim SH, Beratan DN, Tao N. Conductance and configuration of molecular gold-water-gold junctions under electric fields. MATTER 2020; 3:166-179. [PMID: 33103114 PMCID: PMC7584381 DOI: 10.1016/j.matt.2020.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.
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Affiliation(s)
- Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Lead contact
| | - Peng Zhang
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Chaoren Liu
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Xin He
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Haipeng B. Li
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Zixiao Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Joshua Hihath
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David N. Beratan
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes. Biomolecules 2020; 10:biom10050759. [PMID: 32414092 PMCID: PMC7277481 DOI: 10.3390/biom10050759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 01/29/2023] Open
Abstract
Many microbes that survive in cold environments are known to secrete ice-binding proteins (IBPs). The structure–function relationship of these proteins remains unclear. A microbial IBP denoted AnpIBP was recently isolated from a cold-adapted fungus, Antarctomyces psychrotrophicus. The present study identified an orbital illumination (prism ring) on a globular single ice crystal when soaked in a solution of fluorescent AnpIBP, suggesting that AnpIBP binds to specific water molecules located in the ice prism planes. In order to examine this unique ice-binding mechanism, we carried out X-ray structural analysis and mutational experiments. It appeared that AnpIBP is made of 6-ladder β-helices with a triangular cross section that accompanies an “ice-like” water network on the ice-binding site. The network, however, does not exist in a defective mutant. AnpIBP has a row of four unique hollows on the IBS, where the distance between the hollows (14.7 Å) is complementary to the oxygen atom spacing of the prism ring. These results suggest the structure of AnpIBP is fine-tuned to merge with the ice–water interface of an ice crystal through its polygonal water network and is then bound to a specific set of water molecules constructing the prism ring to effectively halt the growth of ice.
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Tsuda S, Yamauchi A, Khan NMMU, Arai T, Mahatabuddin S, Miura A, Kondo H. Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration. Biomolecules 2020; 10:biom10030423. [PMID: 32182859 PMCID: PMC7175324 DOI: 10.3390/biom10030423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 01/01/2023] Open
Abstract
The concentration of a protein is highly related to its biochemical properties, and is a key determinant for its biotechnological applications. Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) are structurally diverse macromolecules that are capable of binding to embryonic ice crystals below 0 °C, making them useful as protectants of ice-block formation. In this study, we examined the maximal solubility of native AFP I–III and AFGP with distilled water, and evaluated concentration dependence of their ice-binding property. Approximately 400 mg/mL (AFP I), 200 mg/mL (AFP II), 100 mg/mL (AFP III), and >1800 mg/mL (AFGP) of the maximal solubility were estimated, and among them AFGP’s solubility is much higher compared with that of ordinary proteins, such as serum albumin (~500 mg/mL). The samples also exhibited unexpectedly high thermal hysteresis values (2–3 °C) at 50–200 mg/mL. Furthermore, the analysis of fluorescence-based ice plane affinity showed that AFP II binds to multiple ice planes in a concentration-dependent manner, for which an oligomerization mechanism was hypothesized. The difference of concentration dependence between AFPs and AFGPs may provide a new clue to help us understand the ice-binding function of these proteins.
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Affiliation(s)
- Sakae Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (A.Y.); (N.M.-M.U.K.); (T.A.); (H.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
- OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8563, Japan
- Correspondence: ; Tel.: +81-11-857-8912
| | - Akari Yamauchi
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (A.Y.); (N.M.-M.U.K.); (T.A.); (H.K.)
| | - N. M.-Mofiz Uddin Khan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (A.Y.); (N.M.-M.U.K.); (T.A.); (H.K.)
| | - Tatsuya Arai
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (A.Y.); (N.M.-M.U.K.); (T.A.); (H.K.)
| | - Sheikh Mahatabuddin
- Department of Nutrition and Food Engineering, Daffodil International University, Dhanmondi, Dhaka 1207, Bangladesh;
| | - Ai Miura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
| | - Hidemasa Kondo
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (A.Y.); (N.M.-M.U.K.); (T.A.); (H.K.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
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Xiang H, Yang X, Ke L, Hu Y. The properties, biotechnologies, and applications of antifreeze proteins. Int J Biol Macromol 2020; 153:661-675. [PMID: 32156540 DOI: 10.1016/j.ijbiomac.2020.03.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023]
Abstract
By natural selection, organisms evolve different solutions to cope with extremely cold weather. The emergence of an antifreeze protein gene is one of the most momentous solutions. Antifreeze proteins possess an importantly functional ability for organisms to survive in cold environments and are widely found in various cold-tolerant species. In this review, we summarize the origin of antifreeze proteins, describe the diversity of their species-specific properties and functions, and highlight the related biotechnology on the basis of both laboratory tests and bioinformatics analysis. The most recent advances in the applications of antifreeze proteins are also discussed. We expect that this systematic review will contribute to the comprehensive knowledge of antifreeze proteins to readers.
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Affiliation(s)
- Hong Xiang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Xiaohu Yang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Lei Ke
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Yong Hu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology.
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de Las Rivas M, Paul Daniel EJ, Narimatsu Y, Compañón I, Kato K, Hermosilla P, Thureau A, Ceballos-Laita L, Coelho H, Bernadó P, Marcelo F, Hansen L, Maeda R, Lostao A, Corzana F, Clausen H, Gerken TA, Hurtado-Guerrero R. Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3. Nat Chem Biol 2020; 16:351-360. [PMID: 31932717 PMCID: PMC7923394 DOI: 10.1038/s41589-019-0444-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 11/09/2022]
Abstract
Polypeptide GalNAc-transferase T3 (GalNAc-T3) regulates fibroblast growth factor 23 (FGF23) by O-glycosylating Thr178 in a furin proprotein processing motif RHT178R↓S. FGF23 regulates phosphate homeostasis and deficiency in GALNT3 or FGF23 results in hyperphosphatemia and familial tumoral calcinosis. We explored the molecular mechanism for GalNAc-T3 glycosylation of FGF23 using engineered cell models and biophysical studies including kinetics, molecular dynamics and X-ray crystallography of GalNAc-T3 complexed to glycopeptide substrates. GalNAc-T3 uses a lectin domain mediated mechanism to glycosylate Thr178 requiring previous glycosylation at Thr171. Notably, Thr178 is a poor substrate site with limiting glycosylation due to substrate clashes leading to destabilization of the catalytic domain flexible loop. We suggest GalNAc-T3 specificity for FGF23 and its ability to control circulating levels of intact FGF23 is achieved by FGF23 being a poor substrate. GalNAc-T3's structure further reveals the molecular bases for reported disease-causing mutations. Our findings provide an insight into how GalNAc-T isoenzymes achieve isoenzyme-specific nonredundant functions.
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Affiliation(s)
- Matilde de Las Rivas
- BIFI, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | | | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logroño, Spain
| | - Kentaro Kato
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
- Department of Eco-epidemiology, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan
| | - Pablo Hermosilla
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | | | - Laura Ceballos-Laita
- BIFI, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Helena Coelho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Nova de Lisboa, Caparica, Portugal
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale. INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Nova de Lisboa, Caparica, Portugal
| | - Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Ryota Maeda
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
- Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logroño, Spain
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Thomas A Gerken
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Ramon Hurtado-Guerrero
- BIFI, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain.
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark.
- Fundación ARAID, Zaragoza, Spain.
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Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry. Biomolecules 2020; 10:biom10020274. [PMID: 32053888 PMCID: PMC7072191 DOI: 10.3390/biom10020274] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023] Open
Abstract
More than 80% of Earth’s surface is exposed periodically or continuously to temperatures below 5 °C. Organisms that can live in these areas are called psychrophilic or psychrotolerant. They have evolved many adaptations that allow them to survive low temperatures. One of the most interesting modifications is production of specific substances that prevent living organisms from freezing. Psychrophiles can synthesize special peptides and proteins that modulate the growth of ice crystals and are generally called ice binding proteins (IBPs). Among them, antifreeze proteins (AFPs) inhibit the formation of large ice grains inside the cells that may damage cellular organelles or cause cell death. AFPs, with their unique properties of thermal hysteresis (TH) and ice recrystallization inhibition (IRI), have become one of the promising tools in industrial applications like cryobiology, food storage, and others. Attention of the industry was also caught by another group of IBPs exhibiting a different activity—ice-nucleating proteins (INPs). This review summarizes the current state of art and possible utilizations of the large group of IBPs.
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45
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Non-equilibrium protic and aprotic ionic liquids: Measuring the distance from the equilibrium state. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface. Biomolecules 2019; 9:biom9050162. [PMID: 31035615 PMCID: PMC6572318 DOI: 10.3390/biom9050162] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 01/15/2023] Open
Abstract
Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca2+-dependent species of AFP, however, it has not been clarified how 1 mol of Ca2+-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca2+-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca2+-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca2+-binding site. Firstly, the side-chains of four of the five Ca2+-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca2+-bound state. Second, a Ca2+-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca2+-binding. Third, the Ca2+-binding induces a generation of ice-like clathrate waters around the Ca2+-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca2+-binding enables the ice-binding of this protein.
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47
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Pandey P, Mallajosyula SS. Elucidating the role of key structural motifs in antifreeze glycoproteins. Phys Chem Chem Phys 2019; 21:3903-3917. [PMID: 30702099 DOI: 10.1039/c8cp06743k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Antifreeze glycoproteins (AFGPs) are distinctively riveting class of bio-macromolecules, which endows the survival of organisms inhabiting polar and subpolar regions. These proteins are believed to hinder microscopic freezing by interacting with embryonic ice crystals and precluding their further growth. The underlying molecular mechanism by which AFGPs bind to ice has remained elusive due to insufficient structural characterization, with conflicting hypotheses on the possible binding mode of AFGPs - either via the hydrophobic peptide backbone or via the hydrophilic carbohydrate side chains - when interacting with ice. Chemical synthesis has allowed researchers to access synthetic variants of natural AFGPs. These studies revealed that AFGPs exhibit huge variations in their thermal hysteresis and ice shaping behavior with only slight structural variations, especially to the carbohydrate side chains. Four key structural motifs were identified as crucial to AFGP activity: the presence of a threonine γ-methyl group, an α-glycosidic carbohydrate-protein linkage, an acetylamide group (-NHCOCH3) at the C2 position of the carbohydrate linked to the protein, and the presence of carbohydrate hydroxyl groups. In this study, we use molecular dynamics (MD) simulations to probe the microscopic properties of water accompanying these structural variations of AFGPs. We find that these variations primarily influence the conformation space of AFGPs and also crucially control their hydration dynamics. Owing to the disordered nature of AFGPs we use Markov-state modeling to identify the conformational preferences of AFGPs. The simulations reveal the importance of steric bulk, intra-molecular carbohydrate-protein H-bonds and conformational preferences (α- vs. β-linkages) in controlling the spatial segregation of the hydrophilic and hydrophobic regions of AFGPs. We hypothesize that the hydrophobic component of AFGPs is crucial to their binding to ice, which determines the ice shaping ability of AFGPs. However, the hydrophilic carbohydrate hydroxyl groups and their ability to form water bridges control the subsequent hydration dynamics, which is key to the antifreeze properties. Investigating the tetrahedral order parameter of water molecules around the carbohydrates revealed competition between solute- and bulk-influenced solvent structures, with maximum restructuring being observed in the interfacial region 2.5-4.5 Å away from the AFGPs.
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Affiliation(s)
- Poonam Pandey
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Simkheda, Gandhinagar, Gujarat, India.
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48
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Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes. Sci Rep 2019; 9:2212. [PMID: 30760774 PMCID: PMC6374469 DOI: 10.1038/s41598-018-36546-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Ice recrystallization is a phenomenon observed as the increase in ice crystal size within an already frozen material. Antifreeze proteins (AFPs), a class of proteins capable of arresting ice crystal growth, are known to inhibit this phenomenon even at sub milli-molar concentrations. A tremendous range in the possible applications of AFPs is hence expected in both medical and industrial fields, while a key determinant of the ice recrystallization inhibition (IRI) is hardly understood. Here, IRI efficiency and ice plane affinity were examined for the wild-type AFPI–III, a defective AFPIII isoform, and a fungal AFP isoform. To simplify the IRI analysis using the formal representation of Ostwald-ripening (r3 = r03 + kt), we monitored specific ice grains exhibiting only uniform growth, for which maximum Feret diameter was measured. The cube of an ice grain’s radius (r3) increased proportionately with time (t), and its slope gave the recrystallization rate (k). There was a significant difference in the IRI efficiency between the samples, and the fungal AFP possessing the activity with the smallest amount (0.27 μM) exhibited an affinity to multiple ice planes. These results suggest that the IRI efficiency is maximized when AFPs bind to a whole set of ice planes.
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49
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Parui S, Jana B. Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure. J Phys Chem B 2019; 123:811-824. [PMID: 30605607 DOI: 10.1021/acs.jpcb.8b11172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.
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Affiliation(s)
- Sridip Parui
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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50
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Parui S, Jana B. Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core. J Phys Chem B 2018; 122:9827-9839. [PMID: 30286600 DOI: 10.1021/acs.jpcb.8b05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.
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Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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