1
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Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
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Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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2
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Koculi E, Thirumalai D. Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL. Biochemistry 2021; 60:460-464. [PMID: 33464880 DOI: 10.1021/acs.biochem.0c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nanocage for a short duration. If confinement of the SPs is the mechanism by which GroEL/ES facilitates folding, it follows that the assisted folding rate, relative to the bulk value, should always be enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. On the basis of our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.
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Affiliation(s)
- Eda Koculi
- Department of Biology, Johns Hopkins University, 144 Mudd Hall, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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3
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Taylor MP, Prunty TM, O'Neil CM. All-or-none folding of a flexible polymer chain in cylindrical nanoconfinement. J Chem Phys 2020; 152:094901. [PMID: 33480730 DOI: 10.1063/1.5144818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Geometric confinement of a polymer chain results in a loss of conformational entropy. For a chain that can fold into a compact native state via a first-order-like transition, as is the case for many small proteins, confinement typically provides an entropic stabilization of the folded state, thereby shifting the location of the transition. This allows for the possibility of confinement (entropy) driven folding. Here, we investigate such confinement effects for a flexible square-well-sphere N-mer chain (monomer diameter σ) confined within a long cylindrical pore (diameter D) or a closed cylindrical box (height H = D). We carry out Wang-Landau simulations to construct the density of states, which provides access to the complete thermodynamics of the system. For a wide pore, an entropic stabilization of the folded state is observed. However, as the pore diameter approaches the size of the folded chain (D ∼ N1/3σ), we find a destabilization effect. For pore diameters smaller than the native ground-state, the chain folds into a different, higher energy, ground state ensemble and the T vs D phase diagram displays non-monotonic behavior as the system is forced into different ground states for different ranges of D. In this regime, isothermal reduction of the confinement dimension can induce folding, unfolding, or crystallite restructuring. For the cylindrical box, we find a monotonic stabilization effect with decreasing D. Scaling laws for the confinement free energy in the athermal limit are also investigated.
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Affiliation(s)
- Mark P Taylor
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
| | - Troy M Prunty
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
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4
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Marchetti M, Ronda L, Percudani R, Bettati S. Immobilization of Allantoinase for the Development of an Optical Biosensor of Oxidative Stress States. SENSORS 2019; 20:s20010196. [PMID: 31905788 PMCID: PMC6983136 DOI: 10.3390/s20010196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 02/04/2023]
Abstract
Allantoin, the natural end product of purine catabolism in mammals, is non-enzymatically produced from the scavenging of reactive oxygen species through the degradation of uric acid. Levels of allantoin in biological fluids are sensitively influenced by the presence of free radicals, making this molecule a candidate marker of acute oxidative stress in clinical analyses. With this aim, we exploited allantoinase—the enzyme responsible for allantoin hydrolization in plants and lower organisms—for the development of a biosensor exploiting a fast enzymatic-chemical assay for allantoin quantification. Recombinant allantoinase was entrapped in a wet nanoporous silica gel matrix and its structural properties, function, and stability were characterized through fluorescence spectroscopy and circular dichroism measurements, and compared to the soluble enzyme. Physical immobilization in silica gel minimally influences the structure and the catalytic efficiency of entrapped allantoinase, which can be reused several times and stored for several months with good activity retention. These results, together with the relative ease of the sol-gel preparation and handling, make the encapsulated allantoinase a good candidate for the development of an allantoin biosensor.
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Affiliation(s)
- Marialaura Marchetti
- Centro Interdipartimentale Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (M.M.); (S.B.)
| | - Luca Ronda
- Centro Interdipartimentale Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (M.M.); (S.B.)
- Dipartimento di Medicina e Chirurgia, Università di Parma, Via Gramsci 14, 43126 Parma, Italy
- Correspondence: ; Tel.: +39-0521-905502
| | - Riccardo Percudani
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Via Parco Area delle Scienze 11/A, 43124 Parma, Italy;
| | - Stefano Bettati
- Centro Interdipartimentale Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (M.M.); (S.B.)
- Dipartimento di Medicina e Chirurgia, Università di Parma, Via Gramsci 14, 43126 Parma, Italy
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5
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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6
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Affiliation(s)
- Mark P. Taylor
- Department of Physics, Hiram College, Hiram, Ohio 44234, United States
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7
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Yang W, Hellner B, Baneyx F. Self-Immobilization of Car9 Fusion Proteins within High Surface Area Silica Sol–Gels and Dynamic Control of Protein Release. Bioconjug Chem 2016; 27:2450-2459. [DOI: 10.1021/acs.bioconjchem.6b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Wenlan Yang
- Department of Chemical Engineering, Box
351750, University of Washington, Seattle, Washington 98195, United States
| | - Brittney Hellner
- Department of Chemical Engineering, Box
351750, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Department of Chemical Engineering, Box
351750, University of Washington, Seattle, Washington 98195, United States
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8
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Vaitheeswaran S, Thirumalai D. Entropy and enthalpy of interaction between amino acid side chains in nanopores. J Chem Phys 2014; 141:22D523. [PMID: 25494794 DOI: 10.1063/1.4901204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.
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Affiliation(s)
- S Vaitheeswaran
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
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9
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Kim H, Keasler SJ, Chen B. A nucleation-based method to study hydrophobic interactions under confinement: enhanced hydrophobic association driven by energetic contributions. J Phys Chem B 2014; 118:6875-84. [PMID: 24853272 DOI: 10.1021/jp5027459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel simulation approach was developed and applied to the study of hydrophobic interactions for a small hydrophobic solute pair under confinement. In this method, the aggregation-volume-bias Monte Carlo algorithm, developed originally for nucleation studies, is used to evaluate the association free energy with water molecules for a methane pair through the gradual addition of water molecules into a nanometer-sized sphere. Through a thermodynamic cycle, this method allows for a convenient examination of the free energy difference between two different solvated configurations without sampling any of the configurations in between. The potential of mean force (PMF) for a methane pair under confinement obtained from this method reveals that the stability of the contact pair configuration can be enhanced compared to that in bulk water, which is in agreement with previous studies. Also, constraining the center of this methane pair at the center of this confined volume yields a PMF with a metastable solvent separated configuration, resembling more closely the PMF from the bulk-phase system compared to previous studies in which this solvent-separated minimum was found to be completely absent. A combination with histogram reweighting enables the study of this association behavior at different thermodynamic conditions without additional simulations. From a comprehensive thermodynamic analysis, it is evident that such hydrophobic association, known to be entropically driven in the bulk-phase system at ambient conditions, is entropically favorable only when a suitable range of solvent molecules is added to the confined system. More importantly, the energetic contributions are a favorable factor that explains the enhanced hydrophobic association toward the high number of solvent molecules.
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Affiliation(s)
- Hyunmi Kim
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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10
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Kerkhofs S, Leroux F, Allouche L, Mellaerts R, Jammaer J, Aerts A, Kirschhock CEA, Magusin PCMM, Taulelle F, Bals S, Van Tendeloo G, Martens JA. Single-step alcohol-free synthesis of core–shell nanoparticles of β-casein micelles and silica. RSC Adv 2014. [DOI: 10.1039/c4ra03252g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
β-Casein is wrapped in a thin shell of SiO2 under biocompatible conditions forming hybrid core–shell nanoparticles.
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Affiliation(s)
- Stef Kerkhofs
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- Heverlee, Belgium
| | - Frederic Leroux
- Electron Microscopy for Materials Science (EMAT)
- UAntwerp, Belgium
| | - Lionel Allouche
- Service de R.M.N
- Institut de Chimie
- Université de Strasbourg
- France
| | - Randy Mellaerts
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- Heverlee, Belgium
| | - Jasper Jammaer
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- Heverlee, Belgium
| | - Alexander Aerts
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- Heverlee, Belgium
| | | | | | - Francis Taulelle
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- Heverlee, Belgium
- Tectospin
- Institut Lavoisier
| | - Sara Bals
- Electron Microscopy for Materials Science (EMAT)
- UAntwerp, Belgium
| | | | - Johan A. Martens
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- Heverlee, Belgium
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11
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Engström K, Johnston EV, Verho O, Gustafson KPJ, Shakeri M, Tai CW, Bäckvall JE. Co-immobilization of an enzyme and a metal into the compartments of mesoporous silica for cooperative tandem catalysis: an artificial metalloenzyme. Angew Chem Int Ed Engl 2013; 52:14006-10. [PMID: 24222082 PMCID: PMC4499256 DOI: 10.1002/anie.201306487] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/04/2013] [Indexed: 11/13/2022]
Affiliation(s)
- Karin Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
| | - Eric V Johnston
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
| | - Oscar Verho
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
| | - Karl P J Gustafson
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
| | - Mozaffar Shakeri
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
| | - Cheuk-Wai Tai
- Department of Materials and Environmental Chemistry and Berzeli Center EXSELENT on Porous Material, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
| | - Jan-E Bäckvall
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University10691 Stockholm (Sweden)
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12
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Engström K, Johnston EV, Verho O, Gustafson KPJ, Shakeri M, Tai CW, Bäckvall JE. Co-immobilization of an Enzyme and a Metal into the Compartments of Mesoporous Silica for Cooperative Tandem Catalysis: An Artificial Metalloenzyme. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306487] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Schlipf DM, Rankin SE, Knutson BL. Pore-size dependent protein adsorption and protection from proteolytic hydrolysis in tailored mesoporous silica particles. ACS APPLIED MATERIALS & INTERFACES 2013; 5:10111-10117. [PMID: 24063730 DOI: 10.1021/am402754h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein adsorption and interactions with mesoporous silica are of interest for a broad range of applications including drug delivery, chemical synthesis, biosensors, and bioseparations. A major challenge in designing mesoporous silica supports for tailored protein interaction is the differentiation of protein interactions at the surface of the particle from interactions within the pore, important features when considering mesoporous silica as a protective support for active proteins. In this investigation, the location of Enhanced Green Fluorescent Proteins (EGFPs) adsorbed on tailored mesoporous silica particles is examined as a function of pore diameter using proteolytic hydrolysis to distinguish between accessible and inaccessible proteins. Pore size control is achieved by tuning the hydrothermal aging temperature (60-110 °C) during synthesis, where the synthesis results in 5-15 μm diameter spherical particles appropriate for imaging by confocal scanning laser microscopy (CSLM). In low pH environments, EGFP unfolds within pores and on the surface of particles, rendering it susceptible to proteolytic hydrolysis by the protease Pepsin A. Upon return to neutral pH, un-hydrolyzed EGFP regains its fluorescence and can be visualized within the mesoporous particles. The pore-size dependent loading and protection of EGFP (2.4 nm diameter×4.2 nm) from proteolytic attack by Pepsin A (7.3 nm×3.6 nm×5.4 nm) is demonstrated by the retention of fluorescence in 7.3 nm pores. Larger-pored materials (>9 nm) provide diminishing protection for EGFP, and the protection is greatly reduced with increasing pore size and pore size distribution breadth. Proteolytic hydrolysis is used to delineate the activity of pore-loaded versus surface-bound proteins and to establish that there is an optimal pore diameter for loading EGFP while protecting it from attack by a larger proteolytic enzyme.
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Affiliation(s)
- Daniel M Schlipf
- Department of Chemical and Materials Engineering, University of Kentucky , 177 F. Paul Anderson Tower, Lexington, Kentucky 40506-0046, United States
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14
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Marchetti M, Bruno S, Campanini B, Peracchi A, Mai N, Mozzarelli A. ATP binding to human serine racemase is cooperative and modulated by glycine. FEBS J 2013; 280:5853-63. [PMID: 23992455 DOI: 10.1111/febs.12510] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 11/26/2022]
Abstract
The N-methyl D-aspartate (NMDA) receptors play a key role in excitatory neurotransmission, and control learning, memory and synaptic plasticity. Their activity is modulated by the agonist glutamate and by the co-agonists d-serine and glycine. In the human brain, d-serine is synthesized from l-serine by the dimeric pyridoxal 5'-phosphate-dependent enzyme serine racemase, which also degrades l- and d-serine to pyruvate and ammonia. The dependence of l- and d-serine β-elimination and l-serine racemization activities on ATP concentration was characterized, and was found to be strongly cooperative, with Hill coefficients close to 2 and apparent ATP dissociation constants ranging from 0.22 to 0.41 mm. ATP binding to the holo-enzyme, monitored by the fluorescence changes of the coenzyme, was also determined to be cooperative, with an apparent dissociation constant of 0.24 mm. Glycine, an active-site ligand, increased the serine racemase affinity for ATP by ~ 22-fold, abolishing cooperativity. Conversely, ATP increased the non-cooperative glycine binding 15-fold. These results indicate cross-talk between allosteric and active sites, leading to the stabilization of two alternative protein conformations with ATP affinities of ~ 10 μM and 1.8 mm, as evaluated within the Monod, Wyman and Changeux model. Therefore, intracellular ATP and glycine control d-serine homeostasis, and, indirectly, NMDA receptor activity. Because hyper- and hypo-activation of NMDA receptors are associated with neuropathologies, the development of allosteric drugs modulating serine racemase activity is a promising therapeutic strategy.
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15
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Pattanasiri B, Li YW, Landau DP, Wüst T, Triampo W. Thermodynamics and structural properties of a confined HP protein determined by Wang-Landau simulation. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/454/1/012071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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16
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A comparative study on the stability and structure of two different green fluorescent proteins in organic co-solvent systems. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0579-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Campanini B, Pioselli B, Raboni S, Felici P, Giordano I, D'Alfonso L, Collini M, Chirico G, Bettati S. Role of histidine 148 in stability and dynamics of a highly fluorescent GFP variant. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:770-9. [PMID: 23357652 DOI: 10.1016/j.bbapap.2013.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
The armory of GFP mutants available to biochemists and molecular biologists is huge. Design and selection of mutants are usually driven by tailored spectroscopic properties, but some key aspects of stability, folding and dynamics of selected GFP variants still need to be elucidated. We have prepared, expressed and characterized three H148 mutants of the highly fluorescent variant GFPmut2. H148 is known to be involved in the H-bonding network surrounding the chromophore, and all the three mutants, H148G, H148R and H148K, show increased pKa values of the chromophore. Only H148G GFPmut2 (Mut2G) gave good expression and purification yields, indicating that position 148 is critical for efficient folding in vivo. The chemical denaturation of Mut2G was monitored by fluorescence emission, absorbance and far-UV circular dichroism spectroscopy. The mutation has little effect on the spectroscopic properties of the protein and on its stability in solution. However, the unfolding kinetics of the protein encapsulated in wet nanoporous silica gels, a system that allows to stabilize conformations that are poorly or only transiently populated in solution, indicate that the unfolding pathway of Mut2G is markedly different from the parent molecule. In particular, encapsulation allowed to identify an unfolding intermediate that retains a native-like secondary structure despite a destructured chromophore environment. Thus, H148 is a critical residue not only for the chromophoric and photodynamic properties, but also for the correct folding of GFP, and its substitution has great impact on expression yields and stability of the mature protein.
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Affiliation(s)
- Barbara Campanini
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy.
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18
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Andrews BT, Capraro DT, Sulkowska JI, Onuchic JN, Jennings PA. Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. J Phys Chem Lett 2013; 4:180-188. [PMID: 23525263 PMCID: PMC3601837 DOI: 10.1021/jz301893w] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Topologically complex proteins fold by multiple routes as a result of hard-to-fold regions of the proteins. Oftentimes these regions are introduced into the protein scaffold for function and increase frustration in the otherwise smooth-funneled landscape. Interestingly, while functional regions add complexity to folding landscapes, they may also contribute to a unique behavior referred to as hysteresis. While hysteresis is predicted to be rare, it is observed in various proteins, including proteins containing a unique peptide cyclization to form a fluorescent chromophore as well as proteins containing a knotted topology in their native fold. Here, hysteresis is demonstrated to be a consequence of the decoupling of unfolding events from the isomerization or hula-twist of a chromophore in one protein and the untying of the knot in a second protein system. The question now is- can hysteresis be a marker for the interplay of landscapes where complex folding and functional regions overlap?
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Affiliation(s)
| | - Dominique T. Capraro
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA
| | | | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, 6100 Main Street, Houston TX 77005
| | - Patricia A. Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA
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19
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Chen W, Jin B, Hu YL, Lu Y, Xia XH. Entrapment of protein in nanotubes formed by a nanochannel and ion-channel hybrid structure of anodic alumina. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1001-5. [PMID: 22311804 DOI: 10.1002/smll.201102117] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 11/22/2011] [Indexed: 05/03/2023]
Abstract
The nanochannel (in a porous layer) and ion-channel (in a barrier layer) hybrid structure of anodic alumina is used as a protein-trapping device. The transmembrane potential drives the electromigration of the charged proteins (FITC-labeled) into the nanochannels, but electromigration across the barrier layer is impossible due to the size-exclusion effect. As a result, the proteins can be continuously trapped in the nanochannels.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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20
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Caraglio M, Pelizzola A. Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model. Phys Biol 2012; 9:016006. [PMID: 22313579 DOI: 10.1088/1478-3975/9/1/016006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In a cellular environment, confinement and macromolecular crowding play an important role in thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saitô-Muñoz-Eaton model for protein folding to study the behavior of six different protein structures confined between two walls. Changing the distance 2R between the walls, we found, in accordance with previous studies, two confinement regimes: starting from large R and decreasing R, confinement first enhances the stability of the folded state as long as this is compact and until a given value of R; then a further decrease of R leads to a decrease of folding temperature and folding rate. We found that in the low confinement regime, both unfolding temperatures and logarithm of folding rates scale as R(-γ) where γ values lie in between 1.42 and 2.35.
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Affiliation(s)
- M Caraglio
- Dipartimento di Fisica, CNISM and Center for Computational Studies, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy.
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21
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Doerdelmann T, Kojetin DJ, Baird-Titus JM, Solt LA, Burris TP, Rance M. Structural and biophysical insights into the ligand-free Pitx2 homeodomain and a ring dermoid of the cornea inducing homeodomain mutant. Biochemistry 2012; 51:665-76. [PMID: 22224469 PMCID: PMC3264736 DOI: 10.1021/bi201639x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The homeodomain-containing transcription factor Pitx2 (pituitary homeobox protein 2) is present in many developing embryonic tissues, including the heart. Its homeodomain is responsible for the recognition and binding to target DNA sequences and thus constitutes a major functional unit in the Pitx2 protein. Nuclear magnetic resonance techniques were employed to determine the solution structure of the native Pitx2 homeodomain and a R24H mutant that causes autosomal dominantly inherited ring dermoid of the cornea syndrome. The structures reveal that both isoforms possess the canonical homeodomain fold. However, the R24H mutation results in a 2-fold increase in DNA binding affinity and a 5 °C decrease in thermal stability, while changing the dynamic environment of the homeodomain only locally. When introduced into full-length Pitx2c, the mutation results in an only 25% loss of transactivation activity. Our data correlate well with clinical observations suggesting a milder deficiency for the R24H mutation compared to those of other Pitx2 homeodomain mutations.
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Affiliation(s)
- Thomas Doerdelmann
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Douglas J. Kojetin
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jamie M. Baird-Titus
- College of Mount St. Joseph, Department of Chemistry, 5701 Delhi Road, Cincinnati, OH 45233, USA
| | - Laura A. Solt
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas P. Burris
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Mark Rance
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
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22
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Bosisio C, Quercioli V, Chirico G, D'Alfonso L, Bettati S, Raboni S, Campanini B, Collini M. Effect of the point mutation H148G on GFPmut2 unfolding kinetics by fluorescence spectroscopy. Biophys Chem 2011; 157:24-32. [DOI: 10.1016/j.bpc.2011.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/04/2011] [Accepted: 04/04/2011] [Indexed: 02/09/2023]
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23
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Iwaoka M, Sano N, Hasegawa N, Yokokawa M, Kunigami S, Shirai H. Structural Transitions and Enzymatic Function of Ribonuclease A Encapsulated in Transparent Porous Silica Gel. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Kameta N, Minamikawa H, Someya Y, Yui H, Masuda M, Shimizu T. Confinement effect of organic nanotubes toward green fluorescent protein (GFP) depending on the inner diameter size. Chemistry 2010; 16:4217-23. [PMID: 20235251 DOI: 10.1002/chem.200903413] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Transportation, release behavior, and stability of a green fluorescent protein (GFP, 3x4 nm) in self-assembled organic nanotubes with three different inner diameters (10, 20, and 80 nm) have been studied in terms of novel nanocontainers. Selective immobilization of a fluorescent acceptor dye on the inner surface enabled us to not only visualize the transportation of GFP in the nanochannels but to also detect release of the encapsulated GFP to the bulk solution in real time, based on fluorescence resonance energy transfer (FRET). Obtained diffusion constants and release rates of GFP markedly decreased as the inner diameter of the nanotubes was decreased. An endo-sensing procedure also clarified the dependence of the thermal and chemical stabilities of the GFP on the inner diameters. The GFP encapsulated in the 10 nm nanochannel showed strong resistance to heat and to a denaturant. On the other hand, the 20 nm nanochannel accelerated the denaturation of the encapsulated GFP compared with the rate of denaturation of the free GFP in bulk and the encapsulated GFP in the 80 nm nanochannels. The confinement effect based on rational fitting of the inner diameter to the size of GFP allowed us to store it stably and without denaturation under high temperatures and high denaturant concentrations.
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Affiliation(s)
- Naohiro Kameta
- Nanotube Research Center (NTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
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25
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Quercioli V, Bosisio C, Daglio SC, Rocca F, D'Alfonso L, Collini M, Baldini G, Chirico G, Bettati S, Raboni S, Campanini B. Photoinduced millisecond switching kinetics in the GFPMut2 E222Q mutant. J Phys Chem B 2010; 114:4664-77. [PMID: 20230008 DOI: 10.1021/jp910075b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
New probes for kinetic intracellular measurements in the millisecond range are desirable to monitor protein biochemical dynamics essential for catalysis, allosteric regulation, and signaling. Good candidates to this aim are the photoswitchable mutants of the green fluorescent protein, whose anionic fluorescence, primed by blue light, is markedly enhanced under an additional excitation at a shorter wavelength and relaxes within a few milliseconds. The aim of this report is to study how the brightness enhancement kinetics depends on the physical-chemical and spectroscopic parameters and to provide proof-of-concept experiments for the use of the fluorescence enhancement in conditions in which the protein diffusion is hindered and thereby photobleaching can be a limiting critical issue. Future, direct applications of photochromic mutants for modulated excitation imaging would in fact require such a detailed knowledge. We present here an extensive study of the photoswitching mechanism of the E222Q mutant of GFPMut2 (Mut2Q), pumped by visible 488 nm light and probed at 400-420 nm, as a function of pH, viscosity, temperature, and light intensity. In solution, two characteristic photoswitching times are found by means of modulated double beam fluorescence correlation spectroscopy in the 1-30 ms range, depending on the solution pH. The photoswitching kinetics is solved in terms of the eigenvalues and the eigenvectors of a specific energy diagram and used directly to fit the data, suggesting that the observed photoswitching amplitudes and kinetics are related to a single three-level transition loop. Finally, we give in vitro examples of the use of modulated excitation microscopy, based on fluorescence enhancement amplitude and kinetics detection, on Mut2Q protein samples immobilized in acrylamide gels.
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Affiliation(s)
- Valentina Quercioli
- Dipartimento di Fisica, Università degli Studi di Milano-Bicocca, Piazza della Scienza 3, 20126 Milano, Italy
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26
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Elcock AH. Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 2010; 20:196-206. [PMID: 20167475 DOI: 10.1016/j.sbi.2010.01.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 01/19/2023]
Abstract
In recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded-volume effects in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
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27
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Jiménez-Banzo A, Ragàs X, Abbruzzetti S, Viappiani C, Campanini B, Flors C, Nonell S. Singlet oxygen photosensitisation by GFP mutants: oxygen accessibility to the chromophore. Photochem Photobiol Sci 2010; 9:1336-41. [DOI: 10.1039/c0pp00125b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Luo G, Zhang Q, Del Castillo AR, Urban V, O'Neill H. Characterization of sol-gel-encapsulated proteins using small-angle neutron scattering. ACS APPLIED MATERIALS & INTERFACES 2009; 1:2262-2268. [PMID: 20355861 DOI: 10.1021/am900430v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Entrapment of biomolecules in silica-derived sol-gels has grown into a vibrant area of research since it was originally demonstrated. However, accessing the consequences of entrapment on biomolecules and the gel structure remains a major challenge in characterizing these biohybrid materials. We present the first demonstration that it is possible with small-angle neutron scattering (SANS) to study the conformation of dilute proteins that are entrapped in transparent and dense sol-gels. Using deuterium-labeled green fluorescent protein (GFP) and SANS with contrast variation, we demonstrate that the scattering signatures of the sol-gel and the protein can be separated. Analysis of the scattering curves of the sol-gels using a mass-fractal model shows that the size of the colloidal silica particles and the fractal dimensions of the gels were similar in the absence and presence of protein, demonstrating that GFP did not influence the reaction pathway for the formation of the gel. The major structural difference in the gels was that the pore size was increased 2-fold in the presence of the protein. At the contrast match point for silica, the scattering signal from GFP inside the gel became distinguishable over a wide q range. Simulated scattering curves representing a monomer, end-to-end dimer, and parallel dimer of the protein were calculated and compared to the experimental data. Our results show that the most likely structure of GFP is that of an end-to-end dimer. This approach can be readily applied and holds great potential for the structural characterization of complex biohybrid and other materials.
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Affiliation(s)
- Guangming Luo
- Center for Structural Molecular Biology, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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29
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Altschuler GM, Willison KR. Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin. J R Soc Interface 2009; 5:1391-408. [PMID: 18708324 DOI: 10.1098/rsif.2008.0185] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin folding and unfolding pathways are collated and then re-examined from this perspective, allowing us to determine the position of the CCT intervention on the actin free-energy folding landscape. The essential role for CCT in actin folding is to provide a free-energy contribution from its ATP cycle, which drives actin to fold from a stable, trapped intermediate I3, to a less stable but now productive folding intermediate I2. We develop two hypothetical mechanisms for actin folding founded upon concepts established for the bacterial type I chaperonin GroEL and extend them to the much more complex CCT system of eukaryotes. A new model is presented in which CCT facilitates free-energy transfer through direct coupling of the nucleotide hydrolysis cycle to the phases of actin substrate maturation.
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Affiliation(s)
- Gabriel M Altschuler
- Cancer Research UK Centre for Cell and Molecular Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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30
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Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability. Proc Natl Acad Sci U S A 2008; 105:17636-41. [PMID: 19004772 DOI: 10.1073/pnas.0803990105] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Confinement effects on protein stability are relevant in a number of biological applications ranging from encapsulation in the cylindrical cavity of a chaperonin, translocation through pores, and structure formation in the exit tunnel of the ribosome. Consequently, free energies of interaction between amino acid side chains in restricted spaces can provide insights into factors that control protein stability in nanopores. Using all-atom molecular dynamics simulations, we show that 3 pair interactions between side chains--hydrophobic (Ala-Phe), polar (Ser-Asn) and charged (Lys-Glu)--are substantially altered in hydrophobic, water-filled nanopores, relative to bulk water. When the pore holds water at bulk density, the hydrophobic pair is strongly destabilized and is driven to large separations corresponding to the width and the length of the cylindrical pore. As the water density is reduced, the preference of Ala and Phe to be at the boundary decreases, and the contact pair is preferred. A model that accounts for the volume accessible to Phe and Ala in the solvent-depleted region near the pore boundary explains the simulation results. In the pore, the hydrogen-bonded interactions between Ser and Asn have an enhanced dependence on their relative orientations, as compared with bulk water. When the side chains of Lys and Glu are restrained to be side by side, parallel to each other, then salt bridge formation is promoted in the nanopore. Based on these results, we argue and demonstrate that for a generic amphiphilic sequence, cylindrical confinement is likely to enhance thermodynamic stability relative to the bulk.
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31
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Krol S, Cannone F, Caccia M, Sironi L, Bianchini P, Campanini B, Collini M, Chirico G, Diaspro A. Structural stability of green fluorescent proteins entrapped in polyelectrolyte nanocapsules. JOURNAL OF BIOPHOTONICS 2008; 1:310-319. [PMID: 19343654 DOI: 10.1002/jbio.200810033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Molecules of a green fluorescent protein mutant, GFPmut2, have been immobilized in nanocapsules, assemblies of charged polyelectrolyte multilayers, with the aim to study the effect of protein-polyelectrolyte interactions on the protein stability against chemical denaturation. GFPmut2 proteins turn out to be stabilized and protected against the denaturating action of small chemical compounds. The nanocapsule protective effect on GFPmut2 is likely due to protein interactions with the negatively charged polymers, that induce an increase in the local rigidity of the protein nano-environment. This suggestion is supported by Fluorescence Polarization measurements on GFPmut2 proteins bound to the NC layers.
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Affiliation(s)
- Silke Krol
- LAMBS, MicroScoBiO Research Center and Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
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32
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Zhou HX, Rivas G, Minton AP. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 2008; 37:375-97. [PMID: 18573087 DOI: 10.1146/annurev.biophys.37.032807.125817] [Citation(s) in RCA: 1551] [Impact Index Per Article: 96.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macromolecules over and above steric repulsion, are discussed. Theoretical and experimental approaches to the characterization of crowding- and confinement-induced effects in systems approaching the complexity of living organisms are suggested.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.
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33
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Bosisio C, Quercioli V, Collini M, D'Alfonso L, Baldini G, Bettati S, Campanini B, Raboni S, Chirico G. Protonation and conformational dynamics of GFP mutants by two-photon excitation fluorescence correlation spectroscopy. J Phys Chem B 2008; 112:8806-14. [PMID: 18582099 DOI: 10.1021/jp801164n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
GFP mutants are known to display fluorescence flickering, a process that occurs in a wide time range. Because serine 65, threonine 203, glutamate 222, and histidine 148 have been indicated as key residues in determining the GFP fluorescence photodynamics, we have focused here on the role of histidine 148 and glutamate 222 by studying the fluorescence dynamics of GFPmut2 (S65A, V68L, and S72A GFP) and its H148G (Mut2G) and E222Q (Mut2Q) mutants. Two relaxation components are found in the fluorescence autocorrelation functions of GFPmut2: a 10-100 micros pH-dependent component and a 100-500 micros laser-power-dependent component. The comparison of these three mutants shows that the mutation of histidine 148 to glycine induces a 3-fold increase in the protonation rate, thereby indicating that the protonation-deprotonation of the chromophore occurs via a proton exchange with the solution mediated by the histidine 148 residue. The power-dependent but pH-independent relaxation mode, which is not affected by the E222Q and H148G mutations, is due to an excited-state process that is probably related to conformational rearrangements of the chromophore after the photoexcitation, more than to the chromophore excited-state proton transfer.
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Affiliation(s)
- C Bosisio
- Dipartimento G. Occhialini, Universita di Milano Bicocca
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34
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Knotts TA, Rathore N, de Pablo JJ. An entropic perspective of protein stability on surfaces. Biophys J 2008; 94:4473-83. [PMID: 18326646 PMCID: PMC2480681 DOI: 10.1529/biophysj.107.123158] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 01/22/2008] [Indexed: 11/18/2022] Open
Abstract
The interaction of proteins with surfaces regulates numerous processes in nature, science, and technology. In many applications, it is desirable to place proteins on surfaces in an active state, and tethering represents one manner in which to accomplish this. However, a clear understanding of how tether placement and design affects protein activity is lacking. Available theoretical models predict that proteins will be stabilized when tethered to substrates. Such models suggest that the surface reduces the number of states accessible to the unfolded state of the protein, thereby reducing the entropic cost of folding on the surface compared to the bulk case. Recent studies, however, have shown that this stabilization is not always seen. The purpose of this article is to determine the validity of the theory with a thorough thermodynamic analysis of the folding of peptides attached to surfaces. Configuration-temperature-density-of-states Monte Carlo simulations are used to examine the behavior of four different peptides of different secondary and tertiary structure. It is found that the surface does reduce the entropic cost of folding for tethered peptides, as the theory suggests. This effect, however, does not always translate into improved stability because the surface may also have a destabilizing enthalpic effect. The theory neglects this effect and assumes that the enthalpy of folding is the same on and off the surface. Both the enthalpic and entropic contributions to the stability are found to be topology- and tether-placement-specific; we show that stability cannot be predicted a priori. A detailed analysis of the folding of protein A shows how the same protein can be both stabilized and destabilized on a surface depending upon how the tethering enhances or hinders the ability of the peptide to form correct tertiary structures.
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Affiliation(s)
- Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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35
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Affiliation(s)
- Alessandro Borgia
- Department of Chemistry, Cambridge University, Medical Research Council Centre for Protein Engineering, Cambridge, CB2 1EW, United Kingdom; ,
| | - Philip M. Williams
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
| | - Jane Clarke
- Department of Chemistry, Cambridge University, Medical Research Council Centre for Protein Engineering, Cambridge, CB2 1EW, United Kingdom; ,
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36
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Effects of relative humidity on enzyme activity immobilized in sol–gel-derived silica nanocomposites. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Kameta N, Masuda M, Mizuno G, Morii N, Shimizu T. Supramolecular nanotube endo sensing for a guest protein. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2008; 4:561-5. [PMID: 18384039 DOI: 10.1002/smll.200700710] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Naohiro Kameta
- SORST, Japan Science and Technology Agency (JST) Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
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38
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Zhou HX. Helix formation inside a nanotube: possible influence of backbone-water hydrogen bonding by the confining surface through modulation of water activity. J Chem Phys 2008; 127:245101. [PMID: 18163710 DOI: 10.1063/1.2812282] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent molecular dynamics simulations of Sorin and Pande [J. Am. Chem. Soc. 128, 6316 (2006)] in explicit solvent found that helix formation of an alanine peptide is disfavored inside a nanotube relative to that in bulk solution. Here, we present a theory to quantitatively rationalize their simulation results. The basic idea is that the nonpolar inner surface of the nanotube creates a depletion layer and raises the activity of the confined water. The raised water activity, in turn, stabilizes the coil state through hydrogen bonding with the backbone amides and carbonyls. We account for the influence of water activity on helix formation within the Lifson-Roig theory. With physically reasonable parameters, the dependence of the helical content on the diameter of the nanotube obtained in the simulations is well reproduced.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahasse, Florida 32306, USA.
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39
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Schuler B, Haran G. Protein Folding and Dynamics from Optical Single Molecule Spectroscopy. SINGLE MOLECULES AND NANOTECHNOLOGY 2008. [DOI: 10.1007/978-3-540-73924-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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40
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Zhang SQ, Cheung MS. Manipulating biopolymer dynamics by anisotropic nanoconfinement. NANO LETTERS 2007; 7:3438-3442. [PMID: 17939726 DOI: 10.1021/nl071948v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
How the geometry of nanosized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nanosized confinement may benefit manufacturing pharmaceuticals in biomaterial sciences and medicine. The behavior of biopolymers in nanosized confinement is investigated using coarse-grained models and molecular simulations. Particularly, we address the effects of shapes of a confinement on protein-folding dynamics by measuring folding rates and dissecting structural properties of the transition states in nanosized spheres and ellipsoids. We find that when the form of a confinement resembles the geometrical properties of the transition states, the rates of folding kinetics are most enhanced. This knowledge of shape selectivity in identifying optimal conditions for reactions will have a broad impact in nanotechnology and pharmaceutical sciences.
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Affiliation(s)
- Shao-Qing Zhang
- Department of Physics, University of Houston, 4800 Calhoun Road, Houston, Texas 77204, USA
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41
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Andrews BT, Schoenfish AR, Roy M, Waldo G, Jennings PA. The rough energy landscape of superfolder GFP is linked to the chromophore. J Mol Biol 2007; 373:476-90. [PMID: 17822714 PMCID: PMC2695656 DOI: 10.1016/j.jmb.2007.07.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 07/18/2007] [Accepted: 07/29/2007] [Indexed: 10/22/2022]
Abstract
Many green fluorescent protein (GFP) variants have been developed for use as fluorescent tags, and recently a superfolder GFP (sfGFP) has been developed as a robust folding reporter. This new variant shows increased stability and improved folding kinetics, as well as 100% recovery of native protein after denaturation. Here, we characterize sfGFP, and find that this variant exhibits hysteresis as unfolding and refolding equilibrium titration curves are non-coincident even after equilibration for more than eight half-lives as estimated from kinetic unfolding and refolding studies. This hysteresis is attributed to trapping in a native-like intermediate state. Mutational studies directed towards inhibiting chromophore formation indicate that the novel backbone cyclization is responsible for the hysteresis observed in equilibrium titrations of sfGFP. Slow equilibration and the presence of intermediates imply a rough landscape. However, de novo folding in the absence of the chromophore is dominated by a smoother energy landscape than that sampled during unfolding and refolding of the post-translationally modified polypeptide.
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Affiliation(s)
- Benjamin T. Andrews
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
| | - Andrea R. Schoenfish
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
| | - Melinda Roy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
| | | | - Patricia A. Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0375
- Corresponding author, E-mail:
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Zhou HX. Protein folding in confined and crowded environments. Arch Biochem Biophys 2007; 469:76-82. [PMID: 17719556 PMCID: PMC2223181 DOI: 10.1016/j.abb.2007.07.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/12/2007] [Accepted: 07/12/2007] [Indexed: 11/17/2022]
Abstract
Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10k(B)T but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA.
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43
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Cannone F, Collini M, Chirico G, Baldini G, Bettati S, Campanini B, Mozzarelli A. Environment effects on the oscillatory unfolding kinetics of GFP. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:795-803. [PMID: 17429619 DOI: 10.1007/s00249-007-0160-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 03/13/2007] [Accepted: 03/20/2007] [Indexed: 11/29/2022]
Abstract
The chromophore of a green fluorescent protein (GFP) mutant engineered to enhance emission and stability is known to display erratic switchings among a few of its chemical substates and, in particular, between the anionic A and the neutral N substates, whose difference is associated with a proton exchange and a consequent conformation rearrangement. However, when close to unfolding, the A-N switchings suddenly become very regular as shown by fluorescence oscillations that have been recently observed for molecules embedded in wet silica gel. In order to establish whether the matrix hosting the protein is responsible for these oscillations, we investigated the effect of another medium (silanized surfaces), of a different denaturant (urea) and of cosolvents (D(2)O and glycerol). The occurrence of periodic A-N switchings, in the last milliseconds before GFP unfolding, is observed under all investigated conditions, together with three specific frequency values that characterize the pre-unfolding fluorescence. Urea and guanidinium, the denaturants employed in order to unfold GFP, do not lead to appreciable differences in the observed switching parameters, whereas the different media embedding the protein give rise only to frequency shifts that scale with the viscosity of the host. The periodicity of the GFP A-N switchings and their dependence on cosolvents suggest that they could be associated with oscillatory motions between meta-stable conformations of the beta-barrel surrounding the chromophore near protein unfolding.
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Affiliation(s)
- Fabio Cannone
- Department of Physics, University of Milano-Bicocca, Milan, Italy
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44
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D'Alfonso L, Collini M, Cannone F, Chirico G, Campanini B, Cottone G, Cordone L. GFP-mut2 proteins in trehalose-water matrixes: spatially heterogeneous protein-water-sugar structures. Biophys J 2007; 93:284-93. [PMID: 17416616 PMCID: PMC1914445 DOI: 10.1529/biophysj.106.090621] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report investigations on the properties of nanoenvironments around single-GFP-mut2 proteins in trehalose-water matrixes. Single-GFPmut2 molecules embedded in thin trehalose-water films were characterized in terms of their fluorescence brightness, bleaching dynamics, excited state lifetime, and fluorescence polarization. For each property, sets of approximately 100-150 single molecules have been investigated as a function of trehalose content and hydration. Three distinct and interconverting families of proteins have been found which differ widely in terms of bleaching dynamics, brightness, and fluorescence polarization, whose relative populations sizably depend on sample hydration. The reported results evidence the simultaneous presence of different protein-trehalose-water nanostructures whose rigidity increases by lowering the sample hydration. Such spatial inhomogeneity is in line with the well-known heterogeneous dynamics in supercooled fluids and in nonsolid carbohydrate glasses and gives a pictorial representation of the sharp, sudden reorganization of the above structures after uptake <==>release of water molecules.
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Affiliation(s)
- Laura D'Alfonso
- Dipartimento di Fisica, Università di Milano Bicocca, Milano, Italy
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45
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Baldini G, Cannone F, Chirico G, Collini M, Campanini B, Bettati S, Mozzarelli A. Evidence of discrete substates and unfolding pathways in green fluorescent protein. Biophys J 2006; 92:1724-31. [PMID: 17142282 PMCID: PMC1796838 DOI: 10.1529/biophysj.106.093567] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present evidence of conformational substates of a green fluorescent protein mutant, GFPmut2, and of their relationship with the protein behavior during chemical unfolding. The fluorescence of single molecules, excited by two infrared photons from a pulsed laser, was detected in two separate channels that simultaneously collected the blue or the green emission from the protein chromophore chemical states (anionic or neutral, respectively). Time recording of the fluorescence signals from molecules in the native state shows that the chromophore, an intrinsic probe sensitive to conformational changes, switches between the two states with average rates that are found to assume distinct values, thereby suggesting a multiplicity of protein substates. Furthermore, under denaturing conditions, the chromophore switching rate displays different and reproducible time evolutions that are characterized by discrete unfolding times. The correlation that is found between native molecules' switching rate values and unfolding times appears as direct evidence that GFPmut2 can unfold only along distinct paths that are determined by the initial folded substate of the protein.
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46
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Chirico G, Cannone F, Diaspro A. Unfolding time distribution of GFP by single molecule fluorescence spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:663-74. [PMID: 16786346 DOI: 10.1007/s00249-006-0075-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 05/05/2006] [Accepted: 05/18/2006] [Indexed: 11/27/2022]
Abstract
We have studied the unfolding of single molecules of GFP-mut2 mutant trapped in wet silica gels in a wide range of GuHCl concentration. After the addition of denaturant, the number of fluorescent molecules decreases with unfolding rates (of the order of 0.01 min(-1)) that are in very good agreement with bulk fluorescence and circular dichroism data. Unexpectedly, single molecule experiments show rare fluctuations in the number of fluorescent proteins at equilibrium. On the other hand, although a first approximate description of the number decays can be reasonably performed by single exponential functions, the distributions of the single molecule unfolding times show a maximum at times congruent with 50-100 min up to the denaturation midpoint concentration of [GuHCl] congruent with 2.5 M. A theoretical analysis of the distributions indicates that this feature is a fingerprint of the competition between unfolding and refolding processes when the protein is very far from the midpoint denaturant concentration.
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Affiliation(s)
- G Chirico
- Department of Physics, University of Milano Bicocca, Piazza della Scienza 3, Milano, Italy.
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47
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Cheung MS, Thirumalai D. Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol 2006; 357:632-43. [PMID: 16427652 DOI: 10.1016/j.jmb.2005.12.048] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 12/04/2005] [Accepted: 12/07/2005] [Indexed: 11/20/2022]
Abstract
We have studied the stability and the yield of the folded WW domains in a spherical nanopore to provide insights into the changes in the folding characteristics due to interactions of the polypeptide (SP) with the walls of the pore. Using different models for the interactions between the nanopore and the polypeptide chain we have obtained results that are relevant to a broad range of experiments. (a) In the temperature and the strength of the SP-pore interaction plane (lambda), there are four "phases," namely, the unfolded state, the native state, the molten globule phase (MG), and the surface interaction-stabilized (SIS) state. The MG and SIS states are populated at moderate and large values of lambda, respectively. For a fixed pore size, the folding rates vary non-monotonically as lambda is varied with a maximum at lambda approximately 1 at which the SP-nanopore interaction is comparable to the stability of the native state. At large lambda values, the WW domain is kinetically trapped in the SIS states. Using multiple sequence alignment, we conclude that similar folding mechanism should be observed in other WW domains as well. (b) To mimic the changes in the nature of the allosterically driven SP-GroEL interactions we consider two models for the dynamic Anfinsen cage (DAC). In DAC1, the SP-cavity interaction cycles between hydrophobic (lambda>0) and hydrophilic (lambda=0) with a period tau. The yield of the native state is a maximum for an optimum value of tau=tau(OPT). At tau=tau(OPT), the largest yield of the native state is obtained when tau(H) approximately tau(P) where tau(H)(tau(P)) is the duration for which the cavity is hydrophobic (hydrophilic). Thus, in order to enhance the native state yield, the cycling rate, for a given loading rate of the GroEL nanomachine, should be maximized. In DAC2, the volume of the cavity is doubled (as happens when ATP and GroES bind to GroEL) and the SP-pore interaction simultaneously changes from hydrophobic to hydrophilic. In this case, we find greater increase in yield of the native state compared to DAC1 at all values of tau.
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Affiliation(s)
- Margaret S Cheung
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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48
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Rathore N, Knotts TA, de Pablo JJ. Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations. Biophys J 2005; 90:1767-73. [PMID: 16361344 PMCID: PMC1367325 DOI: 10.1529/biophysj.105.071076] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effects of chaperonin-like cage-induced confinement on protein stability have been studied for molecules of varying sizes and topologies. Minimalist models based on Gō-like interactions are employed for the proteins, and density-of-states-based Monte Carlo simulations are performed to accurately characterize the thermodynamic transitions. This method permits efficient sampling of conformational space and yields precise estimates of free energy and entropic changes associated with protein folding. We find that confinement-driven stabilization is not only dependent on protein size and cage radius, but also on the specific topology. The choice of the confining potential is also shown to have an effect on the observed stabilization and the scaling behavior of the stabilization with respect to the cage size.
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Affiliation(s)
- Nitin Rathore
- Novozymes North America Inc., Franklinton, North Carolina, USA
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49
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Baldini G, Cannone F, Chirico G. Pre-Unfolding Resonant Oscillations of Single Green Fluorescent Protein Molecules. Science 2005; 309:1096-100. [PMID: 16099991 DOI: 10.1126/science.1115001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Fluorescence spectroscopy of a green fluorescent protein mutant at single-molecule resolution has revealed a remarkable oscillatory behavior that can also be driven by applied fields. We show that immediately before unfolding, several periodic oscillations among the chemical substates of the protein chromophore occur. We also show that applied alternating electric or acoustic fields, when tuned to the protein characteristic frequencies, give rise to strong resonance effects.
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Affiliation(s)
- Giancarlo Baldini
- Laboratory for Advanced BioSpectroscopy, Physics Department, and Centro Nazionale delle Ricerche (CNR)-Istituto Nazionale per la Fisica della Materia (INFM), University of Milano-Bicocca, Milano I-20126, Italy.
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50
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Cannone F, Bologna S, Campanini B, Diaspro A, Bettati S, Mozzarelli A, Chirico G. Tracking unfolding and refolding of single GFPmut2 molecules. Biophys J 2005; 89:2033-45. [PMID: 15994904 PMCID: PMC1366706 DOI: 10.1529/biophysj.105.064584] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unfolding and refolding kinetics of >600 single GFPmut2 molecules, entrapped in wet nanoporous silica gels, were followed by monitoring simultaneously the fluorescence emission of the anionic and neutral state of the chromophore, primed by two-photon excitation. The rate of unfolding, induced by guanidinium chloride, was determined by counting the number of single molecules that disappear in fluorescence images, under conditions that do not cause bleaching or photoinduced conversion between chromophore protonation states. The unfolding rate is of the order of 0.01 min(-1), and its dependence on denaturant concentration is very similar to that previously reported for high protein load gels. Upon rinsing the gels with denaturant-free buffer, the GFPmut2 molecules refold with rates >10 min(-1), with an apparently random distribution between neutral and anionic states, that can be very different from the preunfolding equilibrium. A subsequent very slow (lifetime of approximately 70 min) relaxation leads to the equilibrium distribution of the protonation states. This mechanism, involving one or more native-like refolding intermediates, is likely rate limited by conformational rearrangements that are undetectable in circular dichroism experiments. Several unfolding/refolding cycles can be followed on the same molecules, indicating full reversibility of the process and, noticeably, a bias of denaturated molecules toward refolding in the original protonation state.
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Affiliation(s)
- Fabio Cannone
- Department of Physics, University of Milan Bicocca, 20126 Milan, Italy
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