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Chen H, Wang S, Cao Y, Lei H. Molecular Force Sensors for Biological Application. Int J Mol Sci 2024; 25:6198. [PMID: 38892386 PMCID: PMC11173168 DOI: 10.3390/ijms25116198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The mechanical forces exerted by cells on their surrounding microenvironment are known as cellular traction forces. These forces play crucial roles in various biological processes, such as tissue development, wound healing and cell functions. However, it is hard for traditional techniques to measure cellular traction forces accurately because their magnitude (from pN to nN) and the length scales over which they occur (from nm to μm) are extremely small. In order to fully understand mechanotransduction, highly sensitive tools for measuring cellular forces are needed. Current powerful techniques for measuring traction forces include traction force microscopy (TFM) and fluorescent molecular force sensors (FMFS). In this review, we elucidate the force imaging principles of TFM and FMFS. Then we highlight the application of FMFS in a variety of biological processes and offer our perspectives and insights into the potential applications of FMFS.
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Affiliation(s)
- Huiyan Chen
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Shouhan Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Hai Lei
- School of Physics, Zhejiang University, Hangzhou 310027, China
- Institute for Advanced Study in Physics, Zhejiang University, Hangzhou 310027, China
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2
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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [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: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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3
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Morikawa TJ, Nishiyama M, Yoshizawa K, Fujita H, Watanabe TM. Glycine insertion modulates the fluorescence properties of Aequorea victoria green fluorescent protein and its variants in their ambient environment. Biophys Physicobiol 2021; 18:145-158. [PMID: 34178565 PMCID: PMC8214926 DOI: 10.2142/biophysico.bppb-v18.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/27/2021] [Indexed: 12/04/2022] Open
Abstract
The green fluorescent protein (GFP) derived from Pacific Ocean jellyfish is an essential tool in biology. GFP-solvent interactions can modulate the fluorescent property of GFP. We previously reported that glycine insertion is an effective mutation in the yellow variant of GFP, yellow fluorescent protein (YFP). Glycine insertion into one of the β-strands comprising the barrel structure distorts its structure, allowing water molecules to invade near the chromophore, enhancing hydrostatic pressure or solution hydrophobicity sensitivity. However, the underlying mechanism of how glycine insertion imparts environmental sensitivity to YFP has not been elucidated yet. To unveil the relationship between fluorescence and β-strand distortion, we investigated the effects of glycine insertion on the dependence of the optical properties of GFP variants named enhanced-GFP (eGFP) and its yellow (eYFP) and cyan (eCFP) variants with respect to pH, temperature, pressure, and hydrophobicity. Our results showed that the quantum yield decreased depending on the number of inserted glycines in all variants, and the dependence on pH, temperature, pressure, and hydrophobicity was altered, indicating the invasion of water molecules into the β-barrel. Peak shifts in the emission spectrum were observed in glycine-inserted eGFP, suggesting a change of the electric state in the excited chromophore. A comparative investigation of the spectral shift among variants under different conditions demonstrated that glycine insertion rearranged the hydrogen bond network between His148 and the chromophore. The present results provide important insights for further understanding the fluorescence mechanism in GFPs and suggest that glycine insertion could be a potent approach for investigating the relationship between water molecules and the intra-protein chromophore.
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Affiliation(s)
- Takamitsu J Morikawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, Higashiosaka, Osaka 577-8502, Japan
| | - Keiko Yoshizawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
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4
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Photoactivatable fluorescent probes for spatiotemporal-controlled biosensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115811] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Nifosì R, Mennucci B, Filippi C. The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation. Phys Chem Chem Phys 2019; 21:18988-18998. [PMID: 31464320 DOI: 10.1039/c9cp03722e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Computational approaches have to date failed to fully capture the large (about 0.4 eV) excitation energy tuning displayed by the nearly identical anionic chromophore in different green fluorescent protein (GFP) variants. Here, we present a thorough comparative study of a set of proteins in this sub-family, including the most red- (phiYFP) and blue-shifted (mTFP0.7) ones. We employ a classical polarisable embedding through induced dipoles and combine it with time-dependent density functional theory and multireference perturbation theory in order to capture both state-specific induction contributions and the coupling of the polarisation of the protein to the chromophore transition density. The obtained results show that only upon inclusion of both these two effects generated by the mutual polarisation between the chromophore and the protein can the full spectral tuning be replicated. We finally discuss how this mutual polarisation affects the correlation between excitation energies, dipole moment variation, and molecular electrostatic field.
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Affiliation(s)
- Riccardo Nifosì
- NEST, CNR - Istituto Nanoscienze and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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6
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Colloc'h N, Sacquin-Mora S, Avella G, Dhaussy AC, Prangé T, Vallone B, Girard E. Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep 2017; 7:1858. [PMID: 28500341 PMCID: PMC5431840 DOI: 10.1038/s41598-017-02097-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/20/2017] [Indexed: 11/09/2022] Open
Abstract
Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the “heme sliding mechanism”. Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie Univ., CERVOxy team, centre Cyceron, 14000, Caen, France.
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Giovanna Avella
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy.,BIOGEM Research Institute, Ariano Irpino, Italy
| | - Anne-Claire Dhaussy
- CRISTMAT UMR 6508 CNRS ENSICAEN UNICAEN Normandie Univ., 6 bd du Maréchal Juin, 14050, Caen, France
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, 4 avenue de l'Observatoire, 75270, Paris, France
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy
| | - Eric Girard
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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8
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Araujo JV, Rifaie-Graham O, Apebende EA, Bruns N. Self-reporting Polymeric Materials with Mechanochromic Properties. BIO-INSPIRED POLYMERS 2016. [DOI: 10.1039/9781782626664-00354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The mechanical transduction of force onto molecules is an essential feature of many biological processes that results in the senses of touch and hearing, gives important cues for cellular interactions and can lead to optically detectable signals, such as a change in colour, fluorescence or chemoluminescence. Polymeric materials that are able to visually indicate deformation, stress, strain or the occurrence of microdamage draw inspiration from these biological events. The field of self-reporting (or self-assessing) materials is reviewed. First, mechanochromic events in nature are discussed, such as the formation of bruises on skin, the bleeding of a wound, or marine glow caused by dinoflagellates. Then, materials based on force-responsive mechanophores, such as spiropyrans, cyclobutanes, cyclooctanes, Diels–Alder adducts, diarylbibenzofuranone and bis(adamantyl)-1,2-dioxetane are reviewed, followed by mechanochromic blends, chromophores stabilised by hydrogen bonds, and pressure sensors based on ionic interactions between fluorescent dyes and polyelectrolyte brushes. Mechanobiochemistry is introduced as an important tool to create self-reporting hybrid materials that combine polymers with the force-responsive properties of fluorescent proteins, protein FRET pairs, and other biomacromolecules. Finally, dye-filled microcapsules, microvascular networks, and hollow fibres are demonstrated to be important technologies to create damage-indicating coatings, self-reporting fibre-reinforced composites and self-healing materials.
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Affiliation(s)
- Jose V. Araujo
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Omar Rifaie-Graham
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Edward A. Apebende
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
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9
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Jacchetti E, Gabellieri E, Cioni P, Bizzarri R, Nifosì R. Temperature and pressure effects on GFP mutants: explaining spectral changes by molecular dynamics simulations and TD-DFT calculations. Phys Chem Chem Phys 2016; 18:12828-38. [PMID: 27102429 DOI: 10.1039/c6cp01274d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
By combining spectroscopic measurements under high pressure with molecular dynamics simulations and quantum mechanics calculations we investigate how sub-angstrom structural perturbations are able to tune protein function. We monitored the variations in fluorescence output of two green fluorescent protein mutants (termed Mut2 and Mut2Y, the latter containing the key T203Y mutation) subjected to pressures up to 600 MPa, at various temperatures in the 280-320 K range. By performing 150 ns molecular dynamics simulations of the protein structures at various pressures, we evidenced subtle changes in conformation and dynamics around the light-absorbing chromophore. Such changes explain the measured spectral tuning in the case of the sizable 120 cm(-1) red-shift observed for pressurized Mut2Y, but absent in Mut2. Previous work [Barstow et al., Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 13362] on pressure effects on GFP also involved a T203Y mutant. On the basis of cryocooling X-ray crystallography, the pressure-induced fluorescence blue shift at low temperature (77 K) was attributed to key changes in relative conformation of the chromophore and Tyr203 phenol ring. At room temperature, however, a red shift was observed at high pressure, analogous to the one we observe in Mut2Y. Our investigation of structural variations in compressed Mut2Y also explains their result, bridging the gap between low-temperature and room-temperature high-pressure effects.
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10
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Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it. Sci Rep 2016; 6:22342. [PMID: 26956628 PMCID: PMC4783657 DOI: 10.1038/srep22342] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/09/2016] [Indexed: 02/07/2023] Open
Abstract
Fluorescent proteins have been widely used in biology because of their compatibility and varied applications in living specimens. Fluorescent proteins are often undesirably sensitive to intracellular conditions such as pH and ion concentration, generating considerable issues at times. However, harnessing these intrinsic sensitivities can help develop functional probes. In this study, we found that the fluorescence of yellow fluorescent protein (YFP) depends on the protein concentration in the solution and that this dependence can be enhanced by adding a glycine residue in to the YFP; we applied this finding to construct an intracellular protein-crowding sensor. A Förster resonance energy transfer (FRET) pair, involving a cyan fluorescent protein (CFP) insensitive to protein concentration and a glycine-inserted YFP, works as a genetically encoded probe to evaluate intracellular crowding. By measuring the fluorescence of the present FRET probe, we were able to detect dynamic changes in protein crowding in living cells.
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11
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Huang Q, Gruner SM, Kim CU, Mao Y, Wu X, Szebenyi DME. Reduction of lattice disorder in protein crystals by high-pressure cryocooling. J Appl Crystallogr 2016; 49:149-157. [PMID: 26937238 PMCID: PMC4762570 DOI: 10.1107/s1600576715023195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
High-pressure cryocooling (HPC) has been developed as a technique for reducing the damage that frequently occurs when macromolecular crystals are cryocooled at ambient pressure. Crystals are typically pressurized at around 200 MPa and then cooled to liquid nitrogen temperature under pressure; this process reduces the need for penetrating cryoprotectants, as well as the damage due to cryocooling, but does not improve the diffraction quality of the as-grown crystals. Here it is reported that HPC using a pressure above 300 MPa can reduce lattice disorder, in the form of high mosaicity and/or nonmerohedral twinning, in crystals of three different proteins, namely human glutaminase C, the GTP pyrophosphokinase YjbM and the uncharacterized protein lpg1496. Pressure lower than 250 MPa does not induce this transformation, even with a prolonged pressurization time. These results indicate that HPC at elevated pressures can be a useful tool for improving crystal packing and hence the quality of the diffraction data collected from pressurized crystals.
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Affiliation(s)
| | - Sol M. Gruner
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
| | - Chae Un Kim
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Xiaochun Wu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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12
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Abstract
At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.
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13
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Beauzamy L, Nakayama N, Boudaoud A. Flowers under pressure: ins and outs of turgor regulation in development. ANNALS OF BOTANY 2014; 114:1517-33. [PMID: 25288632 PMCID: PMC4204789 DOI: 10.1093/aob/mcu187] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/01/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Turgor pressure is an essential feature of plants; however, whereas its physiological importance is unequivocally recognized, its relevance to development is often reduced to a role in cell elongation. SCOPE This review surveys the roles of turgor in development, the molecular mechanisms of turgor regulation and the methods used to measure turgor and related quantities, while also covering the basic concepts associated with water potential and water flow in plants. Three key processes in flower development are then considered more specifically: flower opening, anther dehiscence and pollen tube growth. CONCLUSIONS Many molecular determinants of turgor and its regulation have been characterized, while a number of methods are now available to quantify water potential, turgor and hydraulic conductivity. Data on flower opening, anther dehiscence and lateral root emergence suggest that turgor needs to be finely tuned during development, both spatially and temporally. It is anticipated that a combination of biological experiments and physical measurements will reinforce the existing data and reveal unexpected roles of turgor in development.
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Affiliation(s)
- Léna Beauzamy
- Reproduction et Développement des Plantes, INRA, CNRS, ENS de Lyon, UCBL Lyon I, 46 Allée d'Italie, 69364 Lyon Cedex 07, France Laboratoire Joliot-Curie, CNRS, ENS de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Naomi Nakayama
- Reproduction et Développement des Plantes, INRA, CNRS, ENS de Lyon, UCBL Lyon I, 46 Allée d'Italie, 69364 Lyon Cedex 07, France Laboratoire Joliot-Curie, CNRS, ENS de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France Institute of Molecular Plant Sciences, University of Edinburgh, Mayfield Rd, King's Buildings, Edinburgh EH9 3JH, UK
| | - Arezki Boudaoud
- Reproduction et Développement des Plantes, INRA, CNRS, ENS de Lyon, UCBL Lyon I, 46 Allée d'Italie, 69364 Lyon Cedex 07, France Laboratoire Joliot-Curie, CNRS, ENS de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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14
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Brantley JN, Bailey CB, Cannon JR, Clark KA, Vanden Bout DA, Brodbelt JS, Keatinge‐Clay AT, Bielawski CW. Mechanically Modulating the Photophysical Properties of Fluorescent Protein Biocomposites for Ratio‐ and Intensiometric Sensors. Angew Chem Int Ed Engl 2014; 53:5088-92. [DOI: 10.1002/anie.201306988] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 01/26/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Johnathan N. Brantley
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Constance B. Bailey
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Joe R. Cannon
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Katie A. Clark
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - David A. Vanden Bout
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Adrian T. Keatinge‐Clay
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA)
| | - Christopher W. Bielawski
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
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15
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Brantley JN, Bailey CB, Cannon JR, Clark KA, Vanden Bout DA, Brodbelt JS, Keatinge-Clay AT, Bielawski CW. Mechanically Modulating the Photophysical Properties of Fluorescent Protein Biocomposites for Ratio- and Intensiometric Sensors. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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van der Linden P, Dobias F, Vitoux H, Kapp U, Jacobs J, Mc Sweeney S, Mueller-Dieckmann C, Carpentier P. Towards a high-throughput system for high-pressure cooling of cryoprotectant-free biological crystals. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714000855] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A prototype of a high-pressure cooling apparatus dedicated to macromolecular crystallography on synchrotrons is reported. The system allows cooling of biological crystals without the addition of penetrating or nonpenetrating exogenous cryoprotectant by transforming the aqueous solvent into high-density amorphous ice at a pressure of 200 MPa. The samples are directly fished from crystallization trays with cryopins specifically designed for the pressurizing device and which are compatible with robotized sample changers on synchrotron beamlines. Optionally, the system allows noble gas derivatization during the high-pressure cooling procedure. Some technical details of the equipment and of the method are described in this article. A representative series of test crystals shows that the system is capable of successfully cooling samples that normally require a wide variety of cryoprotection conditions. The last section focuses on pressure-induced structural modifications of these proteins, which are shown to be few but nevertheless of interest.
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17
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Higashiura A, Ohta K, Masaki M, Sato M, Inaka K, Tanaka H, Nakagawa A. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:989-93. [PMID: 24121354 PMCID: PMC3795570 DOI: 10.1107/s090904951302373x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/22/2013] [Indexed: 06/02/2023]
Abstract
Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.
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Affiliation(s)
- Akifumi Higashiura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazunori Ohta
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Mika Masaki
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Masaru Sato
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Nara 639-1123, Japan
| | | | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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18
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Glycine insertion makes yellow fluorescent protein sensitive to hydrostatic pressure. PLoS One 2013; 8:e73212. [PMID: 24014139 PMCID: PMC3754940 DOI: 10.1371/journal.pone.0073212] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022] Open
Abstract
Fluorescent protein-based indicators for intracellular environment conditions such as pH and ion concentrations are commonly used to study the status and dynamics of living cells. Despite being an important factor in many biological processes, the development of an indicator for the physicochemical state of water, such as pressure, viscosity and temperature, however, has been neglected. We here found a novel mutation that dramatically enhances the pressure dependency of the yellow fluorescent protein (YFP) by inserting several glycines into it. The crystal structure of the mutant showed that the tyrosine near the chromophore flipped toward the outside of the β-can structure, resulting in the entry of a few water molecules near the chromophore. In response to changes in hydrostatic pressure, a spectrum shift and an intensity change of the fluorescence were observed. By measuring the fluorescence of the YFP mutant, we succeeded in measuring the intracellular pressure change in living cell. This study shows a new strategy of design to engineer fluorescent protein indicators to sense hydrostatic pressure.
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19
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Brantley JN, Bailey CB, Wiggins KM, Keatinge-Clay AT, Bielawski CW. Mechanobiochemistry: harnessing biomacromolecules for force-responsive materials. Polym Chem 2013. [DOI: 10.1039/c3py00001j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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20
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Kim CU, Wierman JL, Gillilan R, Lima E, Gruner SM. A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter. J Appl Crystallogr 2012; 46:234-241. [PMID: 23396891 DOI: 10.1107/s0021889812045013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/30/2012] [Indexed: 11/11/2022] Open
Abstract
High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydrated via vapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryo-cooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.
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Affiliation(s)
- Chae Un Kim
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
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21
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Laurent AD, Mironov VA, Chapagain PP, Nemukhin AV, Krylov AI. Exploring structural and optical properties of fluorescent proteins by squeezing: modeling high-pressure effects on the mStrawberry and mCherry red fluorescent proteins. J Phys Chem B 2012; 116:12426-40. [PMID: 22988813 PMCID: PMC3500579 DOI: 10.1021/jp3060944] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Molecular dynamics calculations of pressure effects on mStrawberry and mCherry fluorescent proteins are reported. The simulations reveal that mStrawberry has much floppier structure at atmospheric pressure, as evidenced by larger backbone fluctuations and the coexistence of two conformers that differ by Ser146 orientation. Consequently, pressure increase has a larger effect on mStrawberry, making its structure more rigid and reducing the population of one of the conformers. The most significant effect of pressure increase is in the hydrogen-bonding network between the chromophore and the nearby residues. The quantum-mechanics/molecular mechanics calculations of excitation energies in mStrawberry explain the observed blue shift and identify Lys70 as the residue that has the most pronounced effect on the spectra. The results suggest that pressure increase causes an initial increase of fluorescence yield only for relatively floppy fluorescent proteins, whereas the fluorescent proteins that have more rigid structures have quantum yields close to their maximum. The results suggest that a low quantum yield in fluorescent proteins is dynamic in nature and depends on the range of thermal motions of the chromophore and fluctuations in the H-bonding network rather than on their average structure.
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22
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Pozzi EA, Schwall LR, Jimenez R, Weber JM. Pressure-induced changes in the fluorescence behavior of red fluorescent proteins. J Phys Chem B 2012; 116:10311-6. [PMID: 22861177 PMCID: PMC4022145 DOI: 10.1021/jp306093h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We present an experimental study on the fluorescence behavior of the red fluorescent proteins TagRFP-S, TagRFP-T, mCherry, mOrange2, mStrawberry, and mKO as a function of pressure up to several GPa. TagRFP-S, TagRFP-T, mOrange2, and mStrawberry show an initial increase in fluorescence intensity upon application of pressure above ambient conditions. At higher pressures, the fluorescence intensity decreases dramatically for all proteins under study, probably due to denaturing of the proteins. Small blue shifts in the fluorescence spectra with increasing pressure were seen in all proteins under study, hinting at increased rigidity of the chromophore environment. In addition, mOrange2 and mStrawberry exhibit strong and abrupt changes in their fluorescence spectra at certain pressures. These changes are likely due to structural modifications of the hydrogen bonding environment of the chromophore. The strong differences in behavior between proteins with identical or very similar chromophores highlight how the chromophore environment contributes to pressure-induced behavior of the fluorescence performance.
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Affiliation(s)
- Eric A. Pozzi
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
| | - Linda R. Schwall
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
| | - Ralph Jimenez
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
| | - J. Mathias Weber
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
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23
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Ichimura T, Fujita H, Yoshizawa K, Watanabe TM. Engineering strain-sensitive yellow fluorescent protein. Chem Commun (Camb) 2012; 48:7871-3. [PMID: 22751284 DOI: 10.1039/c2cc32541a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Various biological events including muscle contraction and vesicle transport can be described as a mechanical process. Many of the corresponding proteins are thus required to generate or sense a force. Here we describe a strain-sensitive yellow fluorescent protein (YFP) recombinant that can detect the intramolecular strains these proteins experience.
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Affiliation(s)
- Taro Ichimura
- Laboratory for Comprehensive Bioimaging, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita-shi, Osaka 565-0874, Japan
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24
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Collins MD, Kim CU, Gruner SM. High-pressure protein crystallography and NMR to explore protein conformations. Annu Rev Biophys 2011; 40:81-98. [PMID: 21275639 DOI: 10.1146/annurev-biophys-042910-155304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-pressure methods for solving protein structures by X-ray crystallography and NMR are maturing. These techniques are beginning to impact our understanding of thermodynamic and structural features that define not only the protein's native conformation, but also the higher free energy conformations. The ability of high-pressure methods to visualize these mostly unexplored conformations provides new insight into protein function and dynamics. In this review, we begin with a historical discussion of high-pressure structural studies, with an eye toward early results that paved the way to mapping the multiple conformations of proteins. This is followed by an examination of several recent studies that emphasize different strengths and uses of high-pressure structural studies, ranging from basic thermodynamics to the suggestion of high-pressure structural methods as a tool for protein engineering.
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Affiliation(s)
- Marcus D Collins
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290, USA
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25
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Englich U, Kriksunov IA, Cerione RA, Cook MJ, Gillilan R, Gruner SM, Huang Q, Kim CU, Miller W, Nielsen S, Schuller D, Smith S, Szebenyi DME. Microcrystallography, high-pressure cryocooling and BioSAXS at MacCHESS. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:70-73. [PMID: 21169696 PMCID: PMC3004259 DOI: 10.1107/s0909049510036010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 09/07/2010] [Indexed: 05/29/2023]
Abstract
The Macromolecular Diffraction Facility at the Cornell High Energy Synchrotron Source (MacCHESS) is a national research resource supported by the National Center for Research Resources of the US National Institutes of Health. MacCHESS is pursuing several research initiatives designed to benefit both CHESS users and the wider structural biology community. Three initiatives are presented in further detail: microcrystallography, which aims to improve the collection of diffraction data from crystals a few micrometers across, or small well diffracting regions of inhomogeneous crystals, so as to obtain high-resolution structures; pressure cryocooling, which can stabilize transient structures and reduce lattice damage during the cooling process; and BioSAXS (small-angle X-ray scattering on biological solutions), which can extract molecular shape and other structural information from macromolecules in solution.
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26
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Cioni P, Gabellieri E. Protein dynamics and pressure: what can high pressure tell us about protein structural flexibility? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:934-41. [PMID: 20934540 DOI: 10.1016/j.bbapap.2010.09.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/22/2010] [Accepted: 09/30/2010] [Indexed: 11/25/2022]
Abstract
After a brief overview of NMR and X-ray crystallography studies on protein flexibility under pressure, we summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of the globular fold and modulation of its dynamical structure is analyzed both in terms of a reduction of internal cavities and of the hydration of the polypeptide. The study of the effect of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (ΔV(0)) of azurin and on the internal dynamics of the protein fold under pressure demonstrate that the creation of an internal cavity will enhance the plasticity and lower the stability of the globular structure. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Patrizia Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Via Moruzzi 1, 56100-Pisa, Italy.
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