1
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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [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: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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2
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Caviglia B, Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Petrillo C, Peters J, Sterpone F, Paciaroni A. Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability. J Phys Chem Lett 2024; 15:1435-1441. [PMID: 38291814 DOI: 10.1021/acs.jpclett.3c03351] [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: 02/01/2024]
Abstract
Molecular mechanisms underlying the thermal response of cells remain elusive. On the basis of the recent result that the short-time diffusive dynamics of the Escherichia coli proteome is an excellent indicator of temperature-dependent bacterial metabolism and death, we used neutron scattering (NS) spectroscopy and molecular dynamics (MD) simulations to investigate the sub-nanosecond proteome mobility in psychro-, meso-, and hyperthermophilic bacteria over a wide temperature range. The magnitude of thermal fluctuations, measured by atomic mean square displacements, is similar among all studied bacteria at their respective thermal cell death. Global roto-translational motions turn out to be the main factor distinguishing the bacterial dynamical properties. We ascribe this behavior to the difference in the average proteome net charge, which becomes less negative for increasing bacterial thermal stability. We propose that the chemical-physical properties of the cytoplasm and the global dynamics of the resulting proteome are fine-tuned by evolution to uphold optimal thermal stability conditions.
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Affiliation(s)
- Beatrice Caviglia
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Daniele Di Bari
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Stepan Timr
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, 182 23 Prague, Czech Republic
| | - Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Judith Peters
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique (CNRS), Univ. Grenoble Alpes, 140 Rue de la Physique, 38402 Saint-Martin-d'Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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3
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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [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: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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4
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Carré L, Gonzalez D, Girard É, Franzetti B. Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars. Environ Microbiol 2023; 25:2216-2230. [PMID: 37349893 DOI: 10.1111/1462-2920.16451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.
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Affiliation(s)
- Lorenzo Carré
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Éric Girard
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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5
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Collins T, Feller G. Psychrophilic enzymes: strategies for cold-adaptation. Essays Biochem 2023; 67:701-713. [PMID: 37021674 DOI: 10.1042/ebc20220193] [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: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
Abstract
Psychrophilic organisms thriving at near-zero temperatures synthesize cold-adapted enzymes to sustain cell metabolism. These enzymes have overcome the reduced molecular kinetic energy and increased viscosity inherent to their environment and maintained high catalytic rates by development of a diverse range of structural solutions. Most commonly, they are characterized by a high flexibility coupled with an intrinsic structural instability and reduced substrate affinity. However, this paradigm for cold-adaptation is not universal as some cold-active enzymes with high stability and/or high substrate affinity and/or even an unaltered flexibility have been reported, pointing to alternative adaptation strategies. Indeed, cold-adaptation can involve any of a number of a diverse range of structural modifications, or combinations of modifications, depending on the enzyme involved, its function, structure, stability, and evolutionary history. This paper presents the challenges, properties, and adaptation strategies of these enzymes.
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Affiliation(s)
- Tony Collins
- Department of Biology, Center of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Georges Feller
- Department of Life Sciences, Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, 4000 Liège, Belgium
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6
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Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria. Nat Commun 2022; 13:7861. [PMID: 36543797 PMCID: PMC9772386 DOI: 10.1038/s41467-022-35523-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.
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7
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Tian Y, Ban X, Li C, Gu Z, Li Z. Modulation of Flexible Loops in Catalytic Cavities Reveals the Thermal Activation Mechanism of a Glycogen-Debranching Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13358-13366. [PMID: 36217266 DOI: 10.1021/acs.jafc.2c04487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Some thermophilic enzymes not only exhibit high thermostability at high temperatures but also have an activation effect by thermal incubation. However, the correlations between temperature-induced structural modulation and thermal activation are still unclear. In this study, we selected a thermophilic glycogen-debranching enzyme from Saccharolobus solfataricus STB09 (SsGDE), which was a promising starch-debranching enzyme with a thermal activation property at temperatures ranging from 50 to 70 °C, to explore the thermal activation mechanism. Molecular dynamics simulations were performed for SsGDE at 30, 50, or 70 °C to reveal the temperature dependence of structure modulation and catalytic function. The results revealed that four loops (loop1 313-337, loop2 399-418, loop3 481-513, and loop4 540-574) in SsGDE were reshaped, which made the catalytic cavity more open. The internal residues, including the catalytic triad Asp3631, Glu399, and Asp471, could be exposed, due to the structural modulation, to exert catalytic functions. We proposed that the thermal activation effect of SsGDE was closely associated with the temperature-induced modulation of the catalytic cavity, which paved the way for further engineering enzymes to achieve higher catalytic performance and stability.
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Affiliation(s)
- Yixiong Tian
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
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8
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Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081219. [PMID: 36013398 PMCID: PMC9410259 DOI: 10.3390/life12081219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms.
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9
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Zheng L, Lu H, Zan B, Li S, Liu H, Liu Z, Huang J, Liu Y, Jiang F, Liu Q, Feng Y, Hong L. Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity. Nucleic Acids Res 2022; 50:7529-7544. [PMID: 35766425 PMCID: PMC9303296 DOI: 10.1093/nar/gkac565] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) widely participate in hosts to defend against the invasion of nucleic acids. Compared with the CRISPR-Cas system, which requires a specific motif on the target and can only use RNA as guide, pAgos exhibit precise endonuclease activity on any arbitrary target sequence and can use both RNA and DNA as guide, thus rendering great potential for genome editing applications. Hitherto, most in-depth studies on the structure-function relationship of pAgos were conducted on thermophilic ones, functioning at ∼60 to 100°C, whose structures were, however, determined experimentally at much lower temperatures (20–33°C). It remains unclear whether these low-temperature structures can represent the true conformations of the thermophilic pAgos under their physiological conditions. The present work studied three pAgos, PfAgo, TtAgo and CbAgo, whose physiological temperatures differ significantly (95, 75 and 37°C). By conducting thorough experimental and simulation studies, we found that thermophilic pAgos (PfAgo and TtAgo) adopt a loosely-packed structure with a partially-melted surface at the physiological temperatures, largely different from the compact crystalline structures determined at moderate temperatures. In contrast, the mesophilic pAgo (CbAgo) assumes a compact crystalline structure at its optimal function temperature. Such a partially-disrupted structure endows thermophilic pAgos with great flexibility both globally and locally at the catalytic sites, which is crucial for them to achieve high DNA-cleavage activity. To further prove this, we incubated thermophilic pAgos with urea to purposely disrupt their structures, and the resulting cleavage activity was significantly enhanced below the physiological temperature, even at human body temperature. Further testing of many thermophilic Agos present in various thermophilic prokaryotes demonstrated that their structures are generally disrupted under physiological conditions. Therefore, our findings suggest that the highly dynamical structure with a partially-melted surface, distinct from the low-temperature crystalline structure, could be a general strategy assumed by thermophilic pAgos to achieve the high DNA-cleavage activity.
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Lu
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongjia Liu
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Liu
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Zaccai G, Madern D, Franzetti B. Intracellular molecular dynamics studied by neutron scattering. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227201009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Incoherent neutron scattering experiments have produced important insights into intracellular molecular dynamics in vivo. Selected results highlight the role of water dynamics in cancer and brain cells, as well as cellular adaptation through the evolution of appropriate molecular dynamics, in order to respond to environmental challenges.
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11
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Carré L, Girard É, Franzetti B. Experimental study of proteome halophilicity using nanoDSF: a proof of concept. Extremophiles 2021; 26:1. [PMID: 34878593 DOI: 10.1007/s00792-021-01250-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/30/2021] [Indexed: 10/19/2022]
Abstract
Adaption to environmental conditions is reflected by protein adaptation. In particular, proteins of extremophiles display distinctive traits ensuring functional, structural and dynamical properties under permanently extreme physical and chemical conditions. While it has mostly been studied with approaches focusing on specific proteins, biophysical approaches have also confirmed this link between environmental and protein adaptation at the more complex and diverse scale of the proteome. However, studies of this type remain challenging and often require large amounts of biological material. We report here the use of nanoDSF as a tool to study proteome stability and solubility in cell lysates of the model halophilic archaeon Haloarcula marismortui. Notably, our results show that, as with single halophilic protein studies, proteome stability was correlated to the concentration of NaCl or KCl under which the cells were lysed and hence the proteome exposed. This work highlights that adaptation to environmental conditions can be experimentally observed at the scale of the proteome. Still, we show that the biochemical properties of single halophilic proteins can only be partially extrapolated to the whole proteome.
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Affiliation(s)
- Lorenzo Carré
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Éric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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12
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Xia YL, Li YP, Fu YX, Liu SQ. The Energetic Origin of Different Catalytic Activities in Temperature-Adapted Trypsins. ACS OMEGA 2020; 5:25077-25086. [PMID: 33043186 PMCID: PMC7542600 DOI: 10.1021/acsomega.0c02401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/09/2020] [Indexed: 05/08/2023]
Abstract
Psychrophilic enzymes were always observed to have higher catalytic activity (k cat) than their mesophilic homologs at room temperature, while the origin of this phenomenon remains obscure. Here, we used two different temperature-adapted trypsins, the psychrophilic Atlantic cod trypsin (ACT) and the mesophilic bovine trypsin (BT), as a model system to explore the energetic origin of their different catalytic activities using computational methods. The results reproduce the characteristic changing trends in the activation free energy, activation enthalpy, and activation entropy between the psychrophilic and mesophilic enzymes, where, in particular, the slightly decreased activation free energy of ACT is determined by its considerably reduced activation enthalpy rather than by its more negative activation entropy compared to BT. The calculated electrostatic contributions to the solvation free energies in the reactant state/ground sate (RS/GS) and transition state (TS) show that, going from BT to ACT, the TS stabilization has a predominant effect over the RS stabilization on lowering the activation enthalpy of ACT. Comparison between the solvation energy components reveals a more optimized electrostatic preorganization to the TS in ACT, which provides a larger stabilization to the TS through reducing the reorganization energy, thus resulting in the lower activation enthalpy and hence lower activation free energy of ACT. Thus, it can be concluded that it is the difference in the protein electrostatic environment, and hence its different stabilizing effects on the TS, that brings about the different catalytic activities of different temperature-adapted trypsins.
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Affiliation(s)
- Yuan-Ling Xia
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
- Editorial
Office of Journal of Yunnan University (Natural Sciences Edition), Yunnan University, Kunming 650091, Yunnan, China
| | - Yong-Ping Li
- School
of Agriculture, Yunnan University, Kunming 650091, Yunnan, China
| | - Yun-Xin Fu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
- Human
Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Shu-Qun Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
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13
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Shou K, Sarter M, de Souza NR, de Campo L, Whitten AE, Kuchel PW, Garvey CJ, Stadler AM. Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201507. [PMID: 33204483 PMCID: PMC7657910 DOI: 10.1098/rsos.201507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein-protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and Å length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na+-selective ionophore monensin and the K+-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.
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Affiliation(s)
- Keyun Shou
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Mona Sarter
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
| | - Nicolas R. de Souza
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Liliana de Campo
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Philip W. Kuchel
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J. Garvey
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
- Biofilm—Research Center for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö, Sweden
- Lund Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
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14
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Takizawa H, Iwakiri J, Asai K. RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. BMC Bioinformatics 2020; 21:210. [PMID: 32448174 PMCID: PMC7245837 DOI: 10.1186/s12859-020-3535-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 05/05/2020] [Indexed: 11/22/2022] Open
Abstract
Background Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary structures. Existing methods, however, are not applicable to long RNAs owing to their high computational complexity. Additionally, previous research has suffered from two numerical difficulties: overflow and significant numerical errors. Result In this research, we reduced the computational complexity of calculating the landscape of the probability distribution of secondary structures by introducing a maximum-span constraint. In addition, we resolved numerical computation problems through two techniques: extended logsumexp and accuracy-guaranteed numerical computation. We analyzed the stability of the secondary structures of 16S ribosomal RNAs at various temperatures without overflow. The results obtained are consistent with previous research on thermophilic bacteria, suggesting that our method is applicable in thermal stability analysis. Furthermore, we quantitatively assessed numerical stability using our method.. Conclusion These results demonstrate that the proposed method is applicable to long RNAs..
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Affiliation(s)
- Hiroki Takizawa
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Junichi Iwakiri
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kiyoshi Asai
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan. .,Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
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15
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The molecular dynamics of bacterial spore and the role of calcium dipicolinate in core properties at the sub-nanosecond time-scale. Sci Rep 2020; 10:8265. [PMID: 32427943 PMCID: PMC7237433 DOI: 10.1038/s41598-020-65093-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 11/18/2022] Open
Abstract
Bacterial spores are among the most resistant forms of life on Earth. Their exceptional resistance properties rely on various strategies, among them the core singular structure, organization and hydration. By using elastic incoherent neutron scattering, we probed the dynamics of Bacillus subtilis spores to determine whether core macromolecular motions at the sub-nanosecond timescale could also contribute to their resistance to physical stresses. In addition, in order to better specify the role of the various spore components, we used different mutants lacking essential structure such as the coat (PS4150 mutant), or the calcium dipicolinic acid complex (CaDPA) located in the core (FB122 mutant). PS4150 allows to better probe the core’s dynamics, as proteins of the coat represent an important part of spore proteins, and FB122 gives information about the role of the large CaDPA depot for the mobility of core’s components. We show that core’s macromolecular mobility is not particularly constrained at the sub-nanosecond timescale in spite of its low water content as some dynamical characteristics as force constants are very close to those of vegetative bacteria such as Escherichia coli or to those of fully hydrated proteins. Although the force constants of the coatless mutant are similar to the wild-type’s ones, it has lower mean square displacements (MSDs) at high Q showing that core macromolecules are somewhat more constrained than the rest of spore components. However, no behavior reflecting the glassy state regularly evoked in the literature could be drawn from our data. As hydration and macromolecules’ mobility are highly correlated, the previous assumption, that core low water content might explain spores’ exceptional resistance properties seems unlikely. Thus, we confirm recent theories, suggesting that core water is mostly as free as bulk water and proteins/macromolecules are fully hydrated. The germination of spores leads to a much less stable system with a force constant of 0.1 N/m and MSDs ~2.5 times higher at low Q than in the dormant state. DPA has also an influence on core mobility with a slightly lower force constant for the DPA-less mutant than for the wild-type, and MSDs that are ~ 1.8 times higher on average than for the wild-type at low Q. At high Q, germinated and DPA-less spores were very similar to the wild-type ones, showing that DPA and core compact structure might influence large amplitude motions rather than local dynamics of macromolecules.
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16
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Molecular dynamics in cells: A neutron view. Biochim Biophys Acta Gen Subj 2020; 1864:129475. [DOI: 10.1016/j.bbagen.2019.129475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 11/21/2022]
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17
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Surviving salt fluctuations: stress and recovery in Halobacterium salinarum, an extreme halophilic Archaeon. Sci Rep 2020; 10:3298. [PMID: 32094390 PMCID: PMC7040004 DOI: 10.1038/s41598-020-59681-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/04/2019] [Indexed: 11/18/2022] Open
Abstract
Halophilic proteins subjected to below about 15% salt in vitro denature through misfolding, aggregation and/or precipitation. Halobacteria, however, have been detected in environments of fluctuating salinity such as coastal salterns and even around fresh water springs in the depths of the Dead Sea. In order to identify the underlying mechanisms of low salt survival, we explored the reactivation capacity of Halobacterium (Hbt) salinarum sub-populations after incubation in low salt media and recovery in physiological salt. Respiratory oxygen consumption was assessed in stressed cells and cell viability was estimated by Live/Dead staining and flow cytometry. In vivo neutron scattering experiments showed that the recovery of Hbt salinarum sub-populations exposed to severe low salt conditions is related to a rapid retrieval of functional molecular dynamics in the proteome. In the hypothesis that the observations on Hbt salinarum have wider relevance, they could be of key ecological significance for the dispersion of extremophiles when environmental fluctuations become severe.
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Giordano D, Boubeta FM, di Prisco G, Estrin DA, Smulevich G, Viappiani C, Verde C. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins. Antioxid Redox Signal 2020; 32:396-411. [PMID: 31578873 DOI: 10.1089/ars.2019.7887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Temperature is one of the most important drivers in shaping protein adaptations. Many biochemical and physiological processes are influenced by temperature. Proteins and enzymes from organisms living at low temperature are less stable in comparison to high-temperature adapted proteins. The lower stability is generally due to greater conformational flexibility. Recent Advances: Adaptive changes in the structure of cold-adapted proteins may occur at subunit interfaces, distant from the active site, thus producing energy changes associated with conformational transitions transmitted to the active site by allosteric modulation, valid also for monomeric proteins in which tertiary structural changes may play an essential role. Critical Issues: Despite efforts, the current experimental and computational methods still fail to produce general principles on protein evolution, since many changes are protein and species dependent. Environmental constraints or other biological cellular signals may override the ancestral information included in the structure of the protein, thus introducing inaccuracy in estimates and predictions on the evolutionary adaptations of proteins in response to cold adaptation. Future Directions: In this review, we describe the studies and approaches used to investigate stability and flexibility in the cold-adapted globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. In fact, future research directions will be prescient on more detailed investigation of cold-adapted proteins and the role of fluctuations between different conformational states.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Fernando Martín Boubeta
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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19
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Cal-Sabater P, Caro I, Castro MJ, Cao MJ, Mateo J, Quinto EJ. Flow Cytometry to Assess the Counts and Physiological State of Cronobacter sakazakii Cells after Heat Exposure. Foods 2019; 8:foods8120688. [PMID: 31888256 PMCID: PMC6963341 DOI: 10.3390/foods8120688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen that is associated with outbreaks of neonatal necrotizing enterocolitis, septicaemia, and meningitis. Reconstituted powdered infant formulae is the most common vehicle of infection. The aim of the present study is to gain insight into the physiological states of C. sakazakii cells using flow cytometry to detect the compromised cells, which are viable but non-culturable using plate-based methods, and to evaluate the impact of milk heat treatments on those populations. Dead-cell suspensions as well as heat-treated and non-heat-treated cell suspensions were used. After 60 or 65 °C treatments, the number of compromised cells increased as a result of cells with compromised membranes shifting from the heat-treated suspension. These temperatures were not effective at killing all bacteria but were effective at compromising their membranes. Thus, mild heat treatments are not enough to guarantee the safety of powered infant formulae. Flow cytometry was capable of detecting C. sakazakii’s compromised cells that cannot be detected with classical plate count methods; thus, it could be used as a screening test to decrease the risk derived from the presence of pathogenic viable but non-culturable cells in this food that is intended for newborns’ nutrition.
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Affiliation(s)
- Paloma Cal-Sabater
- Department of Nutrition and Food Science, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (P.C.-S.); (I.C.)
- Department of Nursery, Faculty of Nursery, University of Valladolid, 47005 Valladolid, Spain; (M.J.C.); (M.J.C.)
| | - Irma Caro
- Department of Nutrition and Food Science, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (P.C.-S.); (I.C.)
| | - María J. Castro
- Department of Nursery, Faculty of Nursery, University of Valladolid, 47005 Valladolid, Spain; (M.J.C.); (M.J.C.)
| | - María J. Cao
- Department of Nursery, Faculty of Nursery, University of Valladolid, 47005 Valladolid, Spain; (M.J.C.); (M.J.C.)
| | - Javier Mateo
- Department of Hygiene and Food Technology, Faculty of Veterinary Medicine, University of León, 24071 León, Spain;
| | - Emiliano J. Quinto
- Department of Nutrition and Food Science, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain; (P.C.-S.); (I.C.)
- Correspondence:
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20
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Colgan TJ, Finlay S, Brown MJF, Carolan JC. Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause. BMC Genomics 2019; 20:959. [PMID: 31823732 PMCID: PMC6902353 DOI: 10.1186/s12864-019-6314-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/20/2019] [Indexed: 01/04/2023] Open
Abstract
Background Understanding the mechanisms by which organisms adapt to unfavourable conditions is a fundamental question in ecology and evolutionary biology. One such mechanism is diapause, a period of dormancy typically found in nematodes, fish, crustaceans and insects. This state is a key life-history event characterised by arrested development, suppressed metabolism and increased stress tolerance and allows an organism to avoid prolonged periods of harsh and inhospitable environmental conditions. For some species, diapause is preceded by mating which can have a profound effect on female behaviour, physiology and key biological processes, including immunity. However, our understanding of how mating impacts long-term immunity and whether these effects persist throughout diapause is currently limited. To address this, we explored molecular changes in the haemolymph of the ecologically important pollinator, the buff-tailed bumblebee Bombus terrestris. B. terrestris queens mate prior to entering diapause, a non-feeding period of arrested development that can last 6–9 months. Using mass-spectrometry-based proteomics, we quantified changes in the pre-diapause queen haemolymph after mating, as well as the subsequent protein expression of mated queens during and post-diapause. Results Our analysis identified distinct proteome profiles associated with diapause preparation, maintenance and termination. More specifically, mating pre-diapause was followed by an increase in the abundance of antimicrobial peptides, key effectors of the immune system. Furthermore, we identified the elevated abundance of these proteins to be maintained throughout diapause. This finding was in contrast to the general reduction observed in immune proteins during diapause suggestive of selective immune priming and expression during diapause. Diapause also affected the expression of proteins involved in cuticular maintenance, olfaction, as well as proteins of unknown function, which may have roles in diapause regulation. Conclusions Our results provide clear molecular evidence for the consequences and benefits of mating at the immune level as it precedes the selective increased abundance of antimicrobial peptides that are sustained throughout diapause. In addition, our results provide novel insights into the molecular mechanisms by which bumblebees prepare for, survive, and recover from diapause, insights that may have implications for our general understanding of these processes in other insect groups.
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Affiliation(s)
- Thomas J Colgan
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, County Cork, Ireland. .,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Sive Finlay
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Mark J F Brown
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
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21
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Salvador-Castell M, Golub M, Martinez N, Ollivier J, Peters J, Oger P. The first study on the impact of osmolytes in whole cells of high temperature-adapted microorganisms. SOFT MATTER 2019; 15:8381-8391. [PMID: 31613294 DOI: 10.1039/c9sm01196j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The hyperthermophilic piezophile, Thermococcus barophilus displays a strong stress response characterized by the accumulation of the organic osmolyte, mannosylglycerate during growth under sub-optimal pressure conditions (0.1 MPa). Taking advantage of this known effect, the impact of osmolytes in piezophiles in an otherwise identical cellular context was investigated, by comparing T. barophilus cells grown under low or optimal pressures (40 MPa). Using neutron scattering techniques, we studied the molecular dynamics of live cells of T. barophilus at different pressures and temperatures. We show that in the presence of osmolytes, cells present a higher diffusion coefficient of hydration water and an increase of bulk water motions at a high temperature. In the absence of osmolytes, the T. barophilus cellular dynamics is more responsive to high temperature and high hydrostatic pressure. These results therefore give clear evidence for a protecting effect of osmolytes on proteins.
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22
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Stadler AM, Schneidewind J, Zamponi M, Knieps-Grünhagen E, Gholami S, Schwaneberg U, Rivalta I, Garavelli M, Davari MD, Jaeger KE, Krauss U. Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics. J Phys Chem B 2019; 123:7372-7384. [PMID: 31380636 DOI: 10.1021/acs.jpcb.9b06608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interplay between protein dynamics and catalysis remains a fundamental question in enzymology. We here investigate the ns-timescale dynamics of a light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR), a photoenzyme crucial for chlorophyll synthesis. LPORs catalyze the light-triggered trans addition of a hydride and a proton across the C17═C18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). Because of the lack of an LPOR structure, the global structural and dynamic consequences of LPOR/Pchlide/NADPH ternary complex formation remain elusive. Moreover, photoactivation of LPORs by low-light preillumination is controversially discussed as unequivocal proof for this phenomenon is lacking. By employing quasielastic neutron spectroscopy (QENS), we show that the formation of the ternary holoprotein complex as well as photoactivation lead to progressive rigidification of the protein. These findings are supported by thermostability measurements, which reveal different melting behavior and thermostabilities for the apo- and holoprotein ternary complexes. Molecular dynamics simulations in good agreement with the experimental QENS results suggest that the increased flexibility observed for the apoprotein stems from structural fluctuations of the NADPH and Pchlide substrate binding sites of the enzyme. On the basis of our results, in conjunction with activity and stability measurements, we provide independent proof for LPOR photoactivation, defined as a process that modifies the protein structure and dynamics, resulting in an increased substrate turnover. Our findings advance the structural and dynamic understanding of LPORs and provide a first link between protein dynamics and catalysis for this enzyme class.
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Affiliation(s)
| | | | - Michaela Zamponi
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstr. 1 , 85748 Garching , Germany
| | | | - Samira Gholami
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , D-52074 Aachen , Germany.,DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182 , F-69342 Lyon , France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy.,École Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, Université de Lyon , 46 Allée d'Italie , F-69364 Lyon Cedex 07 , France
| | - Mehdi D Davari
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , D-52074 Aachen , Germany
| | - Karl-Erich Jaeger
- IBG-1: Biotechnologie , Forschungszentrum Jülich GmbH , D-52425 Jülich , Germany
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23
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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24
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Effects of Random Mutagenesis and In Vivo Selection on the Specificity and Stability of a Thermozyme. Catalysts 2019. [DOI: 10.3390/catal9050440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Factors that give enzymes stability, activity, and substrate recognition result from the combination of few weak molecular interactions, which can be difficult to study through rational protein engineering approaches. We used irrational random mutagenesis and in vivo selection to test if a β-glycosidase from the thermoacidophile Saccharolobus solfataricus (Ssβ-gly) could complement an Escherichia coli strain unable to grow on lactose. The triple mutant of Ssβ-gly (S26L, P171L, and A235V) was more active than the wild type at 85 °C, inactivated at this temperature almost 300-fold quicker, and showed a 2-fold higher kcat on galactosides. The three mutations, which were far from the active site, were analyzed to test their effect at the structural level. Improved activity on galactosides was induced by the mutations. The S26L and P171L mutations destabilized the enzyme through the removal of a hydrogen bond and increased flexibility of the peptide backbone, respectively. However, the flexibility added by S26L mutation improved the activity at T > 60 °C. This study shows that random mutagenesis and biological selection allowed the identification of residues that are critical in determining thermal activity, stability, and substrate recognition.
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25
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Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering. Biophys J 2019; 116:1759-1768. [PMID: 31003761 DOI: 10.1016/j.bpj.2019.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 01/06/2023] Open
Abstract
Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.
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26
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Golub M, Guillon V, Gotthard G, Zeller D, Martinez N, Seydel T, Koza MM, Lafaye C, Clavel D, von Stetten D, Royant A, Peters J. Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering. J R Soc Interface 2019; 16:20180848. [PMID: 30836899 DOI: 10.1098/rsif.2018.0848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.
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Affiliation(s)
- Maksym Golub
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Virginia Guillon
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Dominik Zeller
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
| | - Nicolas Martinez
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Tilo Seydel
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Michael M Koza
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Céline Lafaye
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Damien Clavel
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Antoine Royant
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France.,3 European Synchrotron Radiation Facility , 38043 Grenoble , France
| | - Judith Peters
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
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Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs. Proc Natl Acad Sci U S A 2018; 115:1274-1279. [PMID: 29358381 DOI: 10.1073/pnas.1718910115] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Orthologous proteins of species adapted to different temperatures exhibit differences in stability and function that are interpreted to reflect adaptive variation in structural "flexibility." However, quantifying flexibility and comparing flexibility across proteins has remained a challenge. To address this issue, we examined temperature effects on cytosolic malate dehydrogenase (cMDH) orthologs from differently thermally adapted congeners of five genera of marine molluscs whose field body temperatures span a range of ∼60 °C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on KM of cofactor (NADH)] and structural stability (rate of heat denaturation of activity). To determine how these differences depend on flexibilities of overall structure and of regions known to be important in binding and catalysis, we performed molecular dynamics simulation (MDS) analyses. MDS analyses revealed a significant negative correlation between adaptation temperature and heat-induced increase of backbone atom movements [root mean square deviation (rmsd) of main-chain atoms]. Root mean square fluctuations (RMSFs) of movement by individual amino acid residues varied across the sequence in a qualitatively similar pattern among orthologs. Regions of sequence involved in ligand binding and catalysis-termed mobile regions 1 and 2 (MR1 and MR2), respectively-showed the largest values for RMSF. Heat-induced changes in RMSF values across the sequence and, importantly, in MR1 and MR2 were greatest in cold-adapted species. MDS methods are shown to provide powerful tools for examining adaptation of enzymes by providing a quantitative index of protein flexibility and identifying sequence regions where adaptive change in flexibility occurs.
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Abstract
Inspired by Somero's corresponding state principle that relates protein enhanced thermal stability with mechanical rigidity, we deployed state of the art computational techniques (based on atomistic steered molecular dynamics and Hamiltonian-replica exchange simulations) to study the in silico realization of mechanical and thermal unfolding of two homologous Csp proteins that have evolved to thrive in different thermal environments. By complementing recent single-molecule experiments, we unambiguously show that, for these homologues whose structures are very similar, the increased thermal resistance of the thermophilic variant is not associated with an increased mechanical stability. Our approach provides microscopic insights that are otherwise inaccessible to experimental techniques, and explains why the protein weak spots for thermal and mechanical denaturation are distinct.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
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29
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Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proc Natl Acad Sci U S A 2017; 114:9361-9366. [PMID: 28808004 DOI: 10.1073/pnas.1707357114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Internal subnanosecond timescale motions are key for the function of proteins, and are coupled to the surrounding solvent environment. These fast fluctuations guide protein conformational changes, yet their role for protein stability, and for unfolding, remains elusive. Here, in analogy with the Lindemann criterion for the melting of solids, we demonstrate a common scaling of structural fluctuations of lysozyme protein embedded in different environments as the thermal unfolding transition is approached. By combining elastic incoherent neutron scattering and advanced molecular simulations, we show that, although different solvents modify the protein melting temperature, a unique dynamical regime is attained in proximity of thermal unfolding in all solvents that we tested. This solvation shell-independent dynamical regime arises from an equivalent sampling of the energy landscape at the respective melting temperatures. Thus, we propose that a threshold for the conformational entropy provided by structural fluctuations of proteins exists, beyond which thermal unfolding is triggered.
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30
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Peters J, Marion J, Natali F, Kats E, Bicout DJ. The Dynamical Transition of Lipid Multilamellar Bilayers as a Matter of Cooperativity. J Phys Chem B 2017. [PMID: 28650664 DOI: 10.1021/acs.jpcb.7b05167] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study is the application of a two-state model formerly developed by Bicout and Zaccai [ Bicout , D. J. and Zaccai , G. Biophys. J. 2001 , 80 ( 3 ), 1115 - 1123 ] to describe the dynamical transition exhibited in the atomic mean square displacements of biological samples in terms of dynamic and thermodynamic parameters. Data were obtained by elastic incoherent neutron scattering on 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes in various hydration states and on one partially per-deuterated lipid membrane. Fitting the data with the model allowed investigating which parts of lipid molecules were mainly involved in the dynamical transition, heads, tails, or both. Clear differences were found between the fully protonated and partially deuterated membranes. These findings shed light on the question of what is the degree of dynamical cooperativity of the atoms during the transition. Whereas the level of hydration does not significantly affect it, as the dry, the intermediate dry, and fully hydrated membranes all undergo a rather broad transition, the transition of the lipid tails is much sharper and sets in at much lower temperature than that of the heads. Therefore, the dynamical cooperativity appears high among the particles in the tails. Moreover, the transition of the lipid tails has to be completed first before the one of the head groups starts.
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Affiliation(s)
- Judith Peters
- Université Grenoble Alpes , LiPhy, 140 rue de la physique, 38402 Saint Martin d'Hères, France.,Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France
| | - Jérémie Marion
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,Université Grenoble Alpes , IBS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,CNR-IOM, OGG , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France
| | - Efim Kats
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,Landau Institute for Theoretical Physics, RAS , 142432, Chernogolovka, Moscow region, Russia
| | - Dominique J Bicout
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,Biomathématiques et épidémiologie, EPSP - TIMC-IMAG, UMR CNRS 5525, Université Grenoble Alpes , VetAgro Sup Lyon, 69280 Marcy l'Etoile, France
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31
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Katava M, Maccarini M, Villain G, Paciaroni A, Sztucki M, Ivanova O, Madern D, Sterpone F. Thermal activation of 'allosteric-like' large-scale motions in a eukaryotic Lactate Dehydrogenase. Sci Rep 2017; 7:41092. [PMID: 28112231 PMCID: PMC5253740 DOI: 10.1038/srep41092] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/14/2016] [Indexed: 01/22/2023] Open
Abstract
Conformational changes occurring during the enzymatic turnover are essential for the regulation of protein functionality. Individuating the protein regions involved in these changes and the associated mechanical modes is still a challenge at both experimental and theoretical levels. We present here a detailed investigation of the thermal activation of the functional modes and conformational changes in a eukaryotic Lactate Dehydrogenase enzyme (LDH). Neutron Spin Echo spectroscopy and Molecular Dynamics simulations were used to uncover the characteristic length- and timescales of the LDH nanoscale motions in the apo state. The modes involving the catalytic loop and the mobile region around the binding site are activated at room temperature, and match the allosteric reorganisation of bacterial LDHs. In a temperature window of about 15 degrees, these modes render the protein flexible enough and capable of reorganising the active site toward reactive configurations. On the other hand an excess of thermal excitation leads to the distortion of the protein matrix with a possible anti-catalytic effect. Thus, the temperature activates eukaryotic LDHs via the same conformational changes observed in the allosteric bacterial LDHs. Our investigation provides an extended molecular picture of eukaryotic LDH's conformational landscape that enriches the static view based on crystallographic studies alone.
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Affiliation(s)
- Marina Katava
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Marco Maccarini
- Univ. Grenoble Alpes - Laboratoire TIMC/IMAG UMR CNRS 5525, Grenoble Pavillon Taillefer Domaine de la merci, 38700 La Tronche, France
| | - Guillaume Villain
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Universitá di Perugia, via A. Pascoli, 06123 Perugia, Italy
| | - Michael Sztucki
- European Syncrotron Radiation Facility, 6, rue Jules Horowitz, 38042, Grenoble, France
| | - Oxana Ivanova
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Garching, Germany
| | - Dominique Madern
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
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32
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Zaccai G, Natali F, Peters J, Řihová M, Zimmerman E, Ollivier J, Combet J, Maurel MC, Bashan A, Yonath A. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering. Sci Rep 2016; 6:37138. [PMID: 27849042 PMCID: PMC5111069 DOI: 10.1038/srep37138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023] Open
Abstract
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
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Affiliation(s)
- Giuseppe Zaccai
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue Langevin, F-38042 Grenoble, France.,CNR-IOM, OGG, F-38042 Grenoble, France
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble, France.,Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
| | - Martina Řihová
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague, Czech Republic
| | - Ella Zimmerman
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - J Ollivier
- Institut Laue Langevin, F-38042 Grenoble, France
| | - J Combet
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut Charles Sadron, CNRS-UdS, 67034 Strasbourg Cedex 2, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Anat Bashan
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - Ada Yonath
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
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33
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High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes. Sci Rep 2016; 6:32816. [PMID: 27595789 PMCID: PMC5011708 DOI: 10.1038/srep32816] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022] Open
Abstract
Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.
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34
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Paci E, Brockwell DJ, Dougan L. Tuning protein mechanics through an ionic cluster graft from an extremophilic protein. SOFT MATTER 2016; 12:2688-2699. [PMID: 26809452 DOI: 10.1039/c5sm02938d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
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35
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Molecular adaptation and salt stress response of Halobacterium salinarum cells revealed by neutron spectroscopy. Extremophiles 2015; 19:1099-107. [PMID: 26376634 DOI: 10.1007/s00792-015-0782-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/20/2015] [Indexed: 10/23/2022]
Abstract
Halobacterium salinarum is an extreme halophile archaeon with an absolute requirement for a multimolar salt environment. It accumulates molar concentrations of KCl in the cytosol to counterbalance the external osmotic pressure imposed by the molar NaCl. As a consequence, cytosolic proteins are permanently exposed to low water activity and highly ionic conditions. In non-adapted systems, such conditions would promote protein aggregation, precipitation, and denaturation. In contrast, in vitro studies showed that proteins from extreme halophilic cells are themselves obligate halophiles. In this paper, adaptation via dynamics to low-salt stress in H. salinarum cells was measured by neutron scattering experiments coupled with microbiological characterization. The molecular dynamic properties of a proteome represent a good indicator for environmental adaptation and the neutron/microbiology approach has been shown to be well tailored to characterize these modifications. In their natural setting, halophilic organisms often have to face important variations in environmental salt concentration. The results showed deleterious effects already occur in the H. salinarum proteome, even when the external salt concentration is still relatively high, suggesting the onset of survival mechanisms quite early when the environmental salt concentration decreases.
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36
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Calligari PA, Calandrini V, Ollivier J, Artero JB, Härtlein M, Johnson M, Kneller GR. Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6. J Phys Chem B 2015; 119:7860-73. [PMID: 25996652 DOI: 10.1021/acs.jpcb.5b02034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we study dynamical properties of an extremophilic protein, Initiation Factor 6 (IF6), produced by the archeabacterium Methanocaldococcus jannascii, which thrives close to deep-sea hydrothermal vents where temperatures reach 80 °C and the pressure is up to 750 bar. Molecular dynamics simulations (MD) and quasi-elastic neutron scattering (QENS) measurements give new insights into the dynamical properties of this protein with respect to its eukaryotic and mesophilic homologue. Results obtained by MD are supported by QENS data and are interpreted within the framework of a fractional Brownian dynamics model for the characterization of protein relaxation dynamics. IF6 from M. jannaschii at high temperature and pressure shares similar flexibility with its eukaryotic homologue from S. cerevisieae under ambient conditions. This work shows for the first time, to our knowledge, that the very common pattern of corresponding states for thermophilic protein adaptation can be extended to thermo-barophilic proteins. A detailed analysis of dynamic properties and of local structural fluctuations reveals a complex pattern for "corresponding" structural flexibilities. In particular, in the case of IF6, the latter seems to be strongly related to the entropic contribution given by an additional, C-terminal, 20 amino-acid tail which is evolutionary conserved in all mesophilic IF6s.
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Affiliation(s)
- Paolo A Calligari
- †SISSA, International School for Advanced Studies, via Bonomea 265, 34136 Trieste, Italy
| | - Vania Calandrini
- ‡Computational Biophysics, German Research School for Simulation Sciences, Jülich, Germany
| | - Jacques Ollivier
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Jean-Baptiste Artero
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Michael Härtlein
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Mark Johnson
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Gerald R Kneller
- ∥Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, F-45071 Orléans Cedex 2, France.,⊥Synchrotron Soleil, L'Orme de Merisiers, BP 48, 91192 Gif-sur-Yvette, France.,#Université de Orléans, Chateau de la Source-Av. du Parc Floral, 45067 Orléans, France
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37
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Noue ACDL, Peters J, Gervais P, Martinez N, Perrier-Cornet JM, Natali F. Proton dynamics in bacterial spores, a neutron scattering investigation. EPJ WEB OF CONFERENCES 2015. [DOI: 10.1051/epjconf/20158302003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Longo M, Marconi M, Orecchini A, Petrillo C, Monaco G, Calvitti M, Pirisinu I, Romani R, Sacchetti F, Sebastiani F, Zanatta M, Paciaroni A. Terahertz Dynamics in Human Cells and Their Chromatin. J Phys Chem Lett 2014; 5:2177-2181. [PMID: 26279530 DOI: 10.1021/jz500918w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The terahertz dynamics of human cells of the U937 line and their chromatin has been investigated by high-resolution inelastic X-ray scattering. To highlight its dynamical features in situ, nuclear DNA has been stained by uranyl-acetate salt. The general behavior of the collective dynamics of the whole cell is quite similar to that of bulk water, with a nearly wavevector-independent branch located at about 5 meV and a propagating mode with a linear trend corresponding to a speed of sound of 2900 ± 100 m/s. We provide the first experimental evidence for the existence of two branches also in the dispersion curves of chromatin. The high-energy mode displays an acoustic-like behavior with a sound velocity similar to unstained cells, but in this case the branch likely originates from the superposition of intramolecular DNA optic modes. A low-energy optic-like branch, distinctive of the chromatin moiety, is found at about 2.5 meV.
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Affiliation(s)
- M Longo
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ‡Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - M Marconi
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - A Orecchini
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - C Petrillo
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - G Monaco
- §Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - M Calvitti
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - I Pirisinu
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - R Romani
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - F Sacchetti
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ⊥CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - F Sebastiani
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ⊥CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - M Zanatta
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - A Paciaroni
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
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39
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Stadler AM, Unruh T, Namba K, Samatey F, Zaccai G. Correlation between supercoiling and conformational motions of the bacterial flagellar filament. Biophys J 2014; 105:2157-65. [PMID: 24209861 DOI: 10.1016/j.bpj.2013.09.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/02/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022] Open
Abstract
The bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. Various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. We investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. Thermal fluctuations in the straight L- and R-type filaments were measured and compared to the resting state of the wild-type filament. Amplitudes of motion on the picosecond timescale were found to be similar in the different conformational states. Mean-square displacements and protein resilience on the 0.1 ns timescale demonstrate that the L-type state is more flexible and less resilient than the R-type, whereas the wild-type state lies in between. Our results provide strong support that supercoiling of the protofilaments in the flagellar filament is determined by the strength of molecular forces in and between the flagellin subunits.
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Affiliation(s)
- Andreas M Stadler
- Jülich Centre for Neutron Science JCNS (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich, Jülich, Germany.
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40
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Migliardo F, Tallima H, El Ridi R. Rigidity and resistance of larval- and adult schistosomes-medium interface. Biochem Biophys Res Commun 2014; 446:255-60. [PMID: 24589739 DOI: 10.1016/j.bbrc.2014.02.100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 11/25/2022]
Abstract
Schistosomiasis is second only to malaria in prevalence and severity, and is still a major health problem in many tropical countries worldwide with about 200-300 million cases and with more than 800 million people at risk of infection. Based on these data, the World Health Organization recommends fostering research efforts for understanding at any level the mechanisms of the infection and then decreasing the social and economical impact of schistosomiasis. A key role is played by the parasite apical lipid membrane, which is entirely impervious to the surrounding elements of the immune system. We have previously demonstrated that the interaction between schistosomes and surrounding medium is governed by a parasite surface membrane sphingomyelin-based hydrogen barrier. In the present article, the elastic contribution to the total motion as a function of the exchanged wave-vector Q and the mean square displacement values for Schistosoma mansoni larvae and worms and Schistosomahaematobium worms have been evaluated by quasi elastic neutron scattering (QENS). The results point out that S. mansoni larvae show a smaller mean square displacement in comparison to S. mansoni and S. haematobium worms. These values increased by repeating the measurements after one day. These differences, which are analogous to those observed for the diffusion coefficient we previously evaluated, are interpreted in terms of rigidity of the parasite-medium interaction. S. mansoni larvae are the most rigid systems, while S. haematobium worms are the most flexible. In addition, temperature and hypoxia induce a weakening of the schistosome-medium interaction. These evidences are related to the strength of the hydrogen-bonded interaction between parasites and environment that we previously determined. We have shown that S. mansoni worms are characterized by a weakened interaction in respect to the larvae, while the S. haematobium worms more weakly interact with the surrounding medium than S. mansoni. The present QENS analysis allowed us to characterize the rigidity of larval- and adult S. mansoni and S. haematobium-host interface and to relate it to the parasite resistance to the hostile elements of the surrounding medium and to the immune effectors attack.
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Affiliation(s)
- Federica Migliardo
- Department of Physics and Earth Sciences, University of Messina, 98166 Messina, Italy.
| | - Hatem Tallima
- Zoology Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
| | - Rashika El Ridi
- Zoology Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
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41
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Vauclare P, Madern D, Girard E, Gabel F, Zaccai G, Franzetti B. New insights into microbial adaptation to extreme saline environments. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140202001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Sebastiani F, Orecchini A, Paciaroni A, Jasnin M, Zaccai G, Moulin M, Haertlein M, De Francesco A, Petrillo C, Sacchetti F. Collective THz dynamics in living Escherichia coli cells. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Rusevich L, García Sakai V, Franzetti B, Johnson M, Natali F, Pellegrini E, Peters J, Pieper J, Weik M, Zaccai G. Perspectives in biological physics: the nDDB project for a neutron Dynamics Data Bank for biological macromolecules. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:80. [PMID: 23884625 DOI: 10.1140/epje/i2013-13080-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/13/2013] [Accepted: 02/19/2013] [Indexed: 06/02/2023]
Abstract
Neutron spectroscopy provides experimental data on time-dependent trajectories, which can be directly compared to molecular dynamics simulations. Its importance in helping us to understand biological macromolecules at a molecular level is demonstrated by the results of a literature survey over the last two to three decades. Around 300 articles in refereed journals relate to neutron scattering studies of biological macromolecular dynamics, and the results of the survey are presented here. The scope of the publications ranges from the general physics of protein and solvent dynamics, to the biologically relevant dynamics-function relationships in live cells. As a result of the survey we are currently setting up a neutron Dynamics Data Bank (nDDB) with the aim to make the neutron data on biological systems widely available. This will benefit, in particular, the MD simulation community to validate and improve their force fields. The aim of the database is to expose and give easy access to a body of experimental data to the scientific community. The database will be populated with as much of the existing data as possible. In the future it will give value, as part of a bigger whole, to high throughput data, as well as more detailed studies. A range and volume of experimental data will be of interest in determining how quantitatively MD simulations can reproduce trends across a range of systems and to what extent such trends may depend on sample preparation and data reduction and analysis methods. In this context, we strongly encourage researchers in the field to deposit their data in the nDDB.
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Affiliation(s)
- Leonid Rusevich
- ILL, 6, rue Jules Horowitz, BP 156, F-38042 Grenoble Cedex 9, France
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44
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Peters J, Giudici-Orticoni MT, Zaccai G, Guiral M. Dynamics measured by neutron scattering correlates with the organization of bioenergetics complexes in natural membranes from hyperthermophile and mesophile bacteria. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:78. [PMID: 23880731 DOI: 10.1140/epje/i2013-13078-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/01/2013] [Accepted: 02/26/2013] [Indexed: 06/02/2023]
Abstract
Various models on membrane structure and organization of proteins and complexes in natural membranes emerged during the last years. However, the lack of systematic dynamical studies to complement structural investigations hindered the establishment of a more complete picture of these systems. Elastic incoherent neutron scattering gives access to the dynamics on a molecular level and was applied to natural membranes extracted from the hyperthermophile Aquifex aeolicus and the mesophile Wolinella succinogenes bacteria. The results permitted to extract a hierarchy of dynamic flexibility and atomic resilience within the samples, which correlated with the organization of proteins in bioenergetics complexes and the functionality of the membranes.
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Affiliation(s)
- J Peters
- Institut Laue Langevin, 6 rue J. Horowitz, BP 156, F-38042 Grenoble Cedex 9, France.
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45
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Marty V, Jasnin M, Fabiani E, Vauclare P, Gabel F, Trapp M, Peters J, Zaccai G, Franzetti B. Neutron scattering: a tool to detect in vivo thermal stress effects at the molecular dynamics level in micro-organisms. J R Soc Interface 2013; 10:20130003. [PMID: 23446053 DOI: 10.1098/rsif.2013.0003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vivo molecular dynamics in Halobacterium salinarum cells under stress conditions was measured by neutron scattering experiments coupled with microbiological characterization. Molecular dynamics alterations were detected with respect to unstressed cells, reflecting a softening of protein structures consistent with denaturation. The experiments indicated that the neutron scattering method provides a promising tool to study molecular dynamics modifications in the proteome of living cells induced by factors altering protein folds.
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46
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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47
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Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci 2012; 13:11643-11665. [PMID: 23109875 PMCID: PMC3472767 DOI: 10.3390/ijms130911643] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 01/20/2023] Open
Abstract
Psychrophiles, i.e., organisms thriving permanently at near-zero temperatures, synthesize cold-active enzymes to sustain their cell cycle. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. Considering the subtle structural adjustments required for low temperature activity, directed evolution appears to be the most suitable methodology to engineer cold activity in biological catalysts.
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48
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Stadler AM, Garvey CJ, Bocahut A, Sacquin-Mora S, Digel I, Schneider GJ, Natali F, Artmann GM, Zaccai G. Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics. J R Soc Interface 2012; 9:2845-55. [PMID: 22696485 PMCID: PMC3479923 DOI: 10.1098/rsif.2012.0364] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.
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Affiliation(s)
- A M Stadler
- Institute for Complex Systems (ICS-5: Molecular Biophysics), Forschungszentrum Jülich, Jülich, Germany.
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Cipolla A, Delbrassine F, Da Lage JL, Feller G. Temperature adaptations in psychrophilic, mesophilic and thermophilic chloride-dependent alpha-amylases. Biochimie 2012; 94:1943-50. [PMID: 22634328 DOI: 10.1016/j.biochi.2012.05.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/12/2012] [Indexed: 11/15/2022]
Abstract
The functional and structural adaptations to temperature have been addressed in homologous chloride-dependent α-amylases from a psychrophilic Antarctic bacterium, the ectothermic fruit fly, the homeothermic pig and from a thermophilic actinomycete. This series covers nearly all temperatures encountered by living organisms. We report a striking continuum in the functional properties of these enzymes coupled to their structural stability and related to the thermal regime of the source organism. In particular, thermal stability recorded by intrinsic fluorescence, circular dichroism and differential scanning calorimetry appears to be a compromise between the requirement for a stable native state and the proper structural dynamics to sustain the function at the environmental/physiological temperatures. The thermodependence of activity, the kinetic parameters, the activations parameters and fluorescence quenching support these activity-stability relationships in the investigated α-amylases.
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Affiliation(s)
- Alexandre Cipolla
- Laboratory of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
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50
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Stadler AM, Fabiani E, Zaccai G. Changes in molecular dynamics of apomyoglobin during amyloid formation. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/340/1/012092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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