1
|
Liutkus M, Sasselli IR, Rojas AL, Cortajarena AL. Diverse crystalline protein scaffolds through metal-dependent polymorphism. Protein Sci 2024; 33:e4971. [PMID: 38591647 PMCID: PMC11002994 DOI: 10.1002/pro.4971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
As protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations showed that while most of the crystals were the most thermodynamically stable assemblies, some were kinetically trapped states. Thus, crystalline porosity diversity is achieved and controlled with metal coordination, opening a new scope in the application of proteins as biocompatible protein-metal-organic frameworks (POFs). In addition, metal-dependent polymorphic crystals allow direct comparison of metal coordination preferences.
Collapse
Affiliation(s)
- Mantas Liutkus
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
| | - Ivan R. Sasselli
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- Present address:
Centro de Física de Materiales (CFM)CSIC‐UPV/EHUSan SebastiánSpain
| | - Adriana L. Rojas
- Centre for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceBilbaoSpain
| | - Aitziber L. Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
| |
Collapse
|
2
|
Han Q, Su Y, Smith KM, Binns J, Drummond CJ, Darmanin C, Greaves TL. Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids. J Colloid Interface Sci 2023; 650:1393-1405. [PMID: 37480654 DOI: 10.1016/j.jcis.2023.07.045] [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: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/24/2023]
Abstract
Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.
Collapse
Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Yuyu Su
- School of Engineering, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Kate M Smith
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia; Swiss Light Source, Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232 Villigen, Switzerland
| | - Jack Binns
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| |
Collapse
|
3
|
Zalar M, Bye J, Curtis R. Nonspecific Binding of Adenosine Tripolyphosphate and Tripolyphosphate Modulates the Phase Behavior of Lysozyme. J Am Chem Soc 2023; 145:929-943. [PMID: 36608272 PMCID: PMC9853864 DOI: 10.1021/jacs.2c09615] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Adenosine tripolyphosphate (ATP) is a small polyvalent anion that has recently been shown to interact with proteins and have a major impact on assembly processes involved in biomolecular condensate formation and protein aggregation. However, the nature of non-specific protein-ATP interactions and their effects on protein solubility are largely unknown. Here, the binding of ATP to the globular model protein is characterized in detail using X-ray crystallography and nuclear magnetic resonance (NMR). Using NMR, we identified six ATP binding sites on the lysozyme surface, with one known high-affinity nucleic acid binding site and five non-specific previously unknown sites with millimolar affinities that also bind tripolyphosphate (TPP). ATP binding occurs primarily through the polyphosphate moiety, which was confirmed by the X-ray structure of the lysozyme-ATP complex. Importantly, ATP binds preferentially to arginine over lysine in non-specific binding sites. ATP and TPP have similar effects on solution-phase protein-protein interactions. At low salt concentrations, ion binding to lysozyme causes precipitation, while at higher salt concentrations, redissolution occurs. The addition of an equimolar concentration of magnesium to ATP does not alter ATP binding affinities but prevents lysozyme precipitation. These findings have important implications for both protein crystallization and cell biology. Crystallization occurs readily in ATP solutions outside the well-established crystallization window. In the context of cell biology, the findings suggest that ATP binds non-specifically to folded proteins in physiological conditions. Based on the nature of the binding sites identified by NMR, we propose several mechanisms for how ATP binding can prevent the aggregation of natively folded proteins.
Collapse
|
4
|
Fries MR, Conzelmann NF, Günter L, Matsarskaia O, Skoda MWA, Jacobs RMJ, Zhang F, Schreiber F. Bulk Phase Behavior vs Interface Adsorption: Specific Multivalent Cation and Anion Effects on BSA Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:139-150. [PMID: 33393312 DOI: 10.1021/acs.langmuir.0c02618] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Proteins are ubiquitous and play a critical role in many areas from living organisms to protein microchips. In humans, serum albumin has a prominent role in the foreign body response since it is the first protein which will interact with, e.g., an implant or stent. In this study, we focused on the influence of salts (i.e., different cations (Y3+, La3+) and anions (Cl-, I-) on bovine serum albumin (BSA) in terms of its bulk behavior as well as the role of charges for protein adsorption at the solid-liquid interface in order to understand and control the underlying molecular mechanisms and interactions. This is part of our group's effort to gain a deeper understanding of protein-protein and protein-surface interactions in the presence of multivalent ions. In the bulk, we established two new phase diagrams and found not only multivalent cation-triggered phase transitions, but also a dependence of the protein behavior on the type of anion. The attractive interactions between proteins were observed to increase from Cl- < NO3- < I-, resulting in iodide preventing re-entrant condensation and promoting liquid-liquid phase separation in bulk. Using ellipsometry and a quartz-crystal microbalance with dissipation (QCM-D), we obtained insight into the growth of the protein adsorption layer. Importantly, we found that phase transitions at the substrate can be triggered by certain interface properties, whether they exist in the bulk solution or not. Through the use of a hydrophilic, negatively charged surface (native silica), the direct binding of anions to the interface was prevented. Interestingly, this led to re-entrant adsorption even in the absence of re-entrant condensation in bulk. However, the overall amount of adsorbed protein was enhanced through stronger attractive protein-protein interactions in the presence of iodide salts. These findings illustrate how carefully chosen surface properties and salts can directly steer the binding of anions and cations, which guide protein behavior, thus paving the way for specific/triggered protein-protein, protein-salt, and protein-surface interactions.
Collapse
Affiliation(s)
- Madeleine R Fries
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Nina F Conzelmann
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Luzie Günter
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Olga Matsarskaia
- Institut Max von Laue - Paul Langevin (ILL), CS20156, F-38042 Grenoble, France
| | - Maximilian W A Skoda
- ISIS Facility, STFC, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0QX, United Kingdom
| | - Robert M J Jacobs
- Department for Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Fajun Zhang
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany
- Center for Light-Matter Interaction, Sensors & Analytics LISA+, University of Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
5
|
Ge S, Nemiroski A, Mirica KA, Mace CR, Hennek JW, Kumar AA, Whitesides GM. Magnetic Levitation in Chemistry, Materials Science, and Biochemistry. Angew Chem Int Ed Engl 2020; 59:17810-17855. [PMID: 31165560 DOI: 10.1002/anie.201903391] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Indexed: 12/25/2022]
Abstract
All matter has density. The recorded uses of density to characterize matter date back to as early as ca. 250 BC, when Archimedes was believed to have solved "The Puzzle of The King's Crown" using density.[1] Today, measurements of density are used to separate and characterize a range of materials (including cells and organisms), and their chemical and/or physical changes in time and space. This Review describes a density-based technique-magnetic levitation (which we call "MagLev" for simplicity)-developed and used to solve problems in the fields of chemistry, materials science, and biochemistry. MagLev has two principal characteristics-simplicity, and applicability to a wide range of materials-that make it useful for a number of applications (for example, characterization of materials, quality control of manufactured plastic parts, self-assembly of objects in 3D, separation of different types of biological cells, and bioanalyses). Its simplicity and breadth of applications also enable its use in low-resource settings (for example-in economically developing regions-in evaluating water/food quality, and in diagnosing disease).
Collapse
Affiliation(s)
- Shencheng Ge
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Alex Nemiroski
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Katherine A Mirica
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Charles R Mace
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Jonathan W Hennek
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Ashok A Kumar
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - George M Whitesides
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, MA, 02138, USA.,Kavli Institute for Bionano Science & Technology, Harvard University, 29 Oxford Street, Cambridge, MA, 02138, USA
| |
Collapse
|
6
|
Ge S, Nemiroski A, Mirica KA, Mace CR, Hennek JW, Kumar AA, Whitesides GM. Magnetische Levitation in Chemie, Materialwissenschaft und Biochemie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201903391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shencheng Ge
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Alex Nemiroski
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Katherine A. Mirica
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Charles R. Mace
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Jonathan W. Hennek
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Ashok A. Kumar
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - George M. Whitesides
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
- Wyss Institute for Biologically Inspired Engineering Harvard University 60 Oxford Street Cambridge MA 02138 USA
- Kavli Institute for Bionano Science & Technology Harvard University 29 Oxford Street Cambridge MA 02138 USA
| |
Collapse
|
7
|
Marchenkova MA, Kuranova IP, Timofeev VI, Boikova AS, Dorovatovskii PV, Dyakova YA, Ilina KB, Pisarevskiy YV, Kovalchuk MV. The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme. J Biomol Struct Dyn 2019; 38:5159-5172. [PMID: 31760865 DOI: 10.1080/07391102.2019.1696706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl2 and CuCl2) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu+2, Ni+2 and Na+1 cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | | | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Yury V Pisarevskiy
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation.,The Faculty of Physics, St. Petersburg State University, St. Petersburg, Russian Federation
| |
Collapse
|
8
|
Abstract
AbstractThe strong, long-range electrostatic forces described by Coulomb's law disappear for ions in water, and the behavior of these ions is instead controlled by their water affinity – a weak, short-range force which arises from their charge density. This was established experimentally in the mid-1980s by size-exclusion chromatography on carefully calibrated Sephadex®G-10 (which measures the effective volume and thus the water affinity of an ion) and by neutron diffraction with isotopic substitution (which measures the density and orientation of water molecules near the diffracting ion and thus its water affinity). These conclusions have been confirmed more recently by molecular dynamics simulations, which explicitly model each individual water molecule. This surprising change in force regime occurs because the oppositely charged ions in aqueous salt solutions exist functionally as ion pairs (separated by 0, 1 or 2 water molecules) as has now been shown by dielectric relaxation spectroscopy; this cancels out the strong long-range electrostatic forces and allows the weak, short-range water affinity effects to come to the fore. This microscopic structure of aqueous salt solutions is not captured by models utilizing a macroscopic dielectric constant. Additionally, the Law of Matching Water Affinity, first described in 1997 and 2004, establishes that contact ion pair formation is controlled by water affinity and is a major determinant of the solubility of charged species since only a net neutral species can change phases.
Collapse
|
9
|
Lanza A, Margheritis E, Mugnaioli E, Cappello V, Garau G, Gemmi M. Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme. IUCRJ 2019; 6:178-188. [PMID: 30867915 PMCID: PMC6400191 DOI: 10.1107/s2052252518017657] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/13/2018] [Indexed: 05/22/2023]
Abstract
Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.
Collapse
Affiliation(s)
- Arianna Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Eleonora Margheritis
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Valentina Cappello
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Gianpiero Garau
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| |
Collapse
|
10
|
Plaza-Garrido M, Salinas-Garcia MC, Camara-Artigas A. Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:480-489. [PMID: 29717719 DOI: 10.1107/s205979831800517x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/02/2018] [Indexed: 11/10/2022]
Abstract
The structure of orthorhombic lysozyme has been obtained at 298 K and pH 4.5 using sodium chloride as the precipitant and in the presence of sodium phosphate at a concentration as low as 5 mM. Crystals belonging to space group P212121 (unit-cell parameters a = 30, b = 56, c = 73 Å, α = β = γ = 90.00°) diffracted to a resolution higher than 1 Å, and the high quality of these crystals permitted the identification of a phosphate ion bound to Arg14 and His15. The binding of this ion produces long-range conformational changes affecting the loop containing Ser60-Asn74. The negatively charged phosphate ion shields the electrostatic repulsion of the positively charged arginine and histidine residues, resulting in higher stability of the phosphate-bound lysozyme. Additionally, a low-humidity orthorhombic variant was obtained at pH 4.5, and comparison with those previously obtained at pH 6.5 and 9.5 shows a 1.5 Å displacement of the fifth α-helix towards the active-site cavity, which might be relevant to protein function. Since lysozyme is broadly used as a model protein in studies related to protein crystallization and amyloid formation, these results indicate that the interaction of some anions must be considered when analysing experiments performed at acidic pH values.
Collapse
Affiliation(s)
- Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain
| | - M Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain
| |
Collapse
|
11
|
Takekiyo T, Yoshimura Y. Suppression and dissolution of amyloid aggregates using ionic liquids. Biophys Rev 2018; 10:853-860. [PMID: 29696571 DOI: 10.1007/s12551-018-0421-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/08/2018] [Indexed: 12/22/2022] Open
Abstract
Amyloid aggregates are composed of protein fibrils with a dominant β-sheet structure, are water-insoluble, and are involved in the pathogenesis of many neurodegenerative diseases. Development of pharmaceuticals to treat these diseases and the design of recovery agents for amyloid-type inclusion bodies require the successful suppression and dissolution of such aggregates. Since ionic liquids (ILs) are composed of both a cation and anion and are known to suppress protein aggregation and to dissolve water-insoluble compounds such as cellulose; they may also have potential use as suppression/dissolution agents for amyloid aggregates. In the following review, we present the suppression and dissolution effects of ILs on amyloid aggregates so far reported. The protein-IL affinity (the ability of ILs to interact with amyloid proteins) was found to be the biochemical basis for ILs' suppression of amyloid formation, and the hydrogen-bonding basicity of ILs might be the basis for their ability to dissolve amyloid aggregates. These findings present the potential of ILs to serve as novel pharmaceuticals to treat neurodegenerative diseases and as recovery agents for various amyloid aggregates.
Collapse
Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa, 239-8686, Japan.
| | - Yukihiro Yoshimura
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa, 239-8686, Japan
| |
Collapse
|
12
|
Molitor C, Bijelic A, Rompel A. The potential of hexatungstotellurate(VI) to induce a significant entropic gain during protein crystallization. IUCRJ 2017; 4:734-740. [PMID: 29123675 PMCID: PMC5668858 DOI: 10.1107/s2052252517012349] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/25/2017] [Indexed: 06/01/2023]
Abstract
The limiting factor in protein crystallography is still the production of high-quality crystals. In this regard, the authors have recently introduced hexatungstotellurate(VI) (TEW) as a new crystallization additive, which proved to be successful within the liquid-liquid phase separation (LLPS) zone. Presented here are comparative crystal structure analyses revealing that protein-TEW binding not only induces and stabilizes crystal contacts, but also exhibits a significant impact on the solvent-driven crystallization entropy, which is the driving force for the crystallization process. Upon the formation of TEW-mediated protein-protein contacts, the release of water molecules from the hydration shells of both molecules, i.e. TEW and the protein, causes a reduced solvent-accessible surface area, leading to a significant gain in solvent entropy. Based on the crystal structures of aurone synthase (in the presence and absence of TEW), insights have also been provided into the formation of a metastable LLPS, which is caused by the formation of protein clusters, representing an ideal starting point in protein crystallization. The results strongly encourage the classification of TEW as a valuable crystallization additive.
Collapse
Affiliation(s)
- Christian Molitor
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| | - Aleksandar Bijelic
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| |
Collapse
|
13
|
Yano YF, Kobayashi Y, Ina T, Nitta K, Uruga T. Hofmeister Anion Effects on Protein Adsorption at an Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9892-9898. [PMID: 27575543 DOI: 10.1021/acs.langmuir.6b02352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hofmeister anion effects on adsorption kinetics of the positively charged lysozyme (pH < pI) at an air-water interface were studied by surface tension measurements and time-resolved X-ray reflectometry. In the salt-free solution, the protein adsorption rate increases with decreasing the net positive charge of lysozyme. When salt ions are dissolved in water, the protein adsorption rate drastically increases, and the rate is following an inverse Hoffmeister series (Br(-) > Cl(-) > F(-)). This is the result of the strongly polarized halide anion Br(-) being attracted to the adsorbed protein layer due to strong interaction with local electric field, while weakly polarized anion F(-) having no ability to penetrate the protein layer. In X-ray reflection studies, we observed that the lysozyme molecules initially adsorbed on the air-water interface have a flat unfolded structure as previously reported in the salt-free solution. In contrast, in the concentrated salt solutions, the lysozyme molecules begin to refold during adsorption. This protein refolding as a result of protein-protein rearrangements may be a precursor phenomenon of crystallization. The refolding is most significant for Cl(-), which is a good crystallization agent, whereas it is less observed for the strongly hydrated F(-). It is widely known in the bulk state that kosmotropic anions tend to precipitate proteins but at the same time stabilize proteins against denaturing. On the other hand, at the air-water interface where adsorbed proteins usually unfold, we observed chaotropic anions strongly bound to proteins that reduce electrostatic repulsion between protein molecules, and subsequently they induce protein refolding whereas the kosmotropic anions do not.
Collapse
Affiliation(s)
- Yohko F Yano
- Department of Physics, Kindai University , 3-4-1 Kowakae, Higashiosaka City, Osaka 577-8502, Japan
| | - Yuki Kobayashi
- Department of Physics, Kindai University , 3-4-1 Kowakae, Higashiosaka City, Osaka 577-8502, Japan
| | - Toshiaki Ina
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cyo, Sayo-gun, Hyogo 679-5198, Japan
| | - Kiyofumi Nitta
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cyo, Sayo-gun, Hyogo 679-5198, Japan
| | - Tomoya Uruga
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cyo, Sayo-gun, Hyogo 679-5198, Japan
| |
Collapse
|
14
|
Takekiyo T, Yamaguchi E, Yoshida K, Kato M, Yamaguchi T, Yoshimura Y. Interaction Site between the Protein Aggregates and Thiocyanate Ion in Aqueous Solution: A Case Study of 1-Butyl-3-methylimidazolium Thiocyanate. J Phys Chem B 2015; 119:6536-44. [DOI: 10.1021/acs.jpcb.5b01650] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takahiro Takekiyo
- Department
of Applied Chemistry, National Defense Academy, 1-10-20 Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan
| | - Erika Yamaguchi
- Department
of Applied Chemistry, National Defense Academy, 1-10-20 Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan
| | - Koji Yoshida
- Department
of Chemistry, Faculty of Science, Fukuoka University, Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0810, Japan
| | - Minoru Kato
- Department
of Pharmacy, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Toshio Yamaguchi
- Department
of Chemistry, Faculty of Science, Fukuoka University, Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0810, Japan
| | - Yukihiro Yoshimura
- Department
of Applied Chemistry, National Defense Academy, 1-10-20 Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan
| |
Collapse
|
15
|
Bijelic A, Molitor C, Mauracher SG, Al-Oweini R, Kortz U, Rompel A. Hen egg-white lysozyme crystallisation: protein stacking and structure stability enhanced by a Tellurium(VI)-centred polyoxotungstate. Chembiochem 2015; 16:233-41. [PMID: 25521080 PMCID: PMC4498469 DOI: 10.1002/cbic.201402597] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 01/24/2023]
Abstract
As synchrotron radiation becomes more intense, detectors become faster and structure-solving software becomes more elaborate, obtaining single crystals suitable for data collection is now the bottleneck in macromolecular crystallography. Hence, there is a need for novel and advanced crystallisation agents with the ability to crystallise proteins that are otherwise challenging. Here, an Anderson-Evans-type polyoxometalate (POM), specifically Na6 [TeW6 O24 ]⋅22 H2 O (TEW), is employed as a crystallisation additive. Its effects on protein crystallisation are demonstrated with hen egg-white lysozyme (HEWL), which co-crystallises with TEW in the vicinity (or within) the liquid-liquid phase separation (LLPS) region. The X-ray structure (PDB ID: 4PHI) determination revealed that TEW molecules are part of the crystal lattice, thus demonstrating specific binding to HEWL with electrostatic interactions and hydrogen bonds. The negatively charged TEW polyoxotungstate binds to sites with a positive electrostatic potential located between two (or more) symmetry-related protein chains. Thus, TEW facilitates the formation of protein-protein interfaces of otherwise repulsive surfaces, and thereby the realisation of a stable crystal lattice. In addition to retaining the isomorphicity of the protein structure, the anomalous scattering of the POMs was used for macromolecular phasing. The results suggest that hexatungstotellurate(VI) has great potential as a crystallisation additive to promote both protein crystallisation and structure elucidation.
Collapse
Affiliation(s)
- Aleksandar Bijelic
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| | - Christian Molitor
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| | - Stephan G Mauracher
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| | - Rami Al-Oweini
- School of Engineering and Science, Jacobs UniversityP. O. Box 750 561, 28725 Bremen (Germany)
| | - Ulrich Kortz
- School of Engineering and Science, Jacobs UniversityP. O. Box 750 561, 28725 Bremen (Germany)
| | - Annette Rompel
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| |
Collapse
|
16
|
Bénas P, Auzeil N, Legrand L, Brachet F, Regazzetti A, Riès-Kautt M. Weak protein-cationic co-ion interactions addressed by X-ray crystallography and mass spectrometry. ACTA ACUST UNITED AC 2014; 70:2217-31. [PMID: 25084340 DOI: 10.1107/s1399004714011304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/15/2014] [Indexed: 11/10/2022]
Abstract
The adsorption of Rb(+), Cs(+), Mn(2+), Co(2+) and Yb(3+) onto the positively charged hen egg-white lysozyme (HEWL) has been investigated by solving 13 X-ray structures of HEWL crystallized with their chlorides and by applying electrospray ionization mass spectrometry (ESI-MS) first to dissolved protein crystals and then to the protein in buffered salt solutions. The number of bound cations follows the order Cs(+) < Mn(2+) ≃ Co(2+) < Yb(3+) at 293 K. HEWL binds less Rb(+) (qtot = 0.7) than Cs(+) (qtot = 3.9) at 100 K. Crystal flash-cooling drastically increases the binding of Cs(+), but poorly affects that of Yb(3+), suggesting different interactions. The addition of glycerol increases the number of bound Yb(3+) cations, but only slightly increases that of Rb(+). HEWL titrations with the same chlorides, followed by ESI-MS analysis, show that only about 10% of HEWL binds Cs(+) and about 40% binds 1-2 Yb(3+) cations, while the highest binding reaches 60-70% for protein binding 1-3 Mn(2+) or Co(2+) cations. The binding sites identified by X-ray crystallography show that the monovalent Rb(+) and Cs(+) preferentially bind to carbonyl groups, whereas the multivalent Mn(2+), Co(2+) and Yb(3+) interact with carboxylic groups. This work elucidates the basis of the effect of the Hofmeister cation series on protein solubility.
Collapse
Affiliation(s)
- Philippe Bénas
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Nicolas Auzeil
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire EA 4463, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Laurent Legrand
- Institut des NanoSciences de Paris (INSP), UMR 7588 CNRS/UPMC (Université Paris 6), 4 Place Jussieu, 75252 Paris CEDEX 05, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Anne Regazzetti
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire EA 4463, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Madeleine Riès-Kautt
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| |
Collapse
|
17
|
Fedotova MV, Kruchinin SE. Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions. Biophys Chem 2014; 190-191:25-31. [DOI: 10.1016/j.bpc.2014.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022]
|
18
|
Kuzmanic A, Zagrovic B. Dependence of protein crystal stability on residue charge states and ion content of crystal solvent. Biophys J 2014; 106:677-86. [PMID: 24507608 PMCID: PMC3944895 DOI: 10.1016/j.bpj.2013.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/22/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022] Open
Abstract
Protein crystallization is frequently induced by the addition of various precipitants, which directly affect protein solubility. In addition to organic cosolvents and long-chain polymers, salts belong to the most widely used precipitants in protein crystallography. However, despite such widespread usage, their mode of action at the atomistic level is still largely unknown. Here, we perform extensive molecular dynamics simulations of the villin headpiece crystal unit cell to examine its stability at different concentrations of sodium sulfate. We show that the inclusion of ions in crystal solvent at high concentration can prevent large rearrangements of the asymmetric units and a loss of symmetry of the unit cell without significantly affecting protein dynamics. Of importance, a similar result can be achieved by neutralizing several specific charged residues suggesting that they may play an active role in crystal destabilization due to unfavorable electrostatic interactions. Our results provide a microscopic picture behind salt-induced stabilization of a protein crystal and further suggest that adequate modeling of realistic crystallization conditions may be necessary for successful molecular dynamics simulations of protein crystals.
Collapse
Affiliation(s)
- Antonija Kuzmanic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
| |
Collapse
|
19
|
In vitro hyperglycemic condition facilitated the aggregation of lysozyme via the passage through a molten globule state. Cell Biochem Biophys 2013. [PMID: 23184703 DOI: 10.1007/s12013-012-9479-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hyperglycemic condition i.e. an increase in blood glucose concentration has been linked to bring about structural alterations in the native state of proteins. Glucose concentrations of 50 and 100 mM in vitro, which correspond to hyperglycemic condition, were tested to investigate their effect on lysozyme native structure. Incubating enzyme with 50 and 100 mM glucose for a period of 7 days, an intermediate state on day 4 and 3 was observed, respectively. The presence of intermediate state was characterized by a 22 % increase in the intrinsic fluorescence intensity with a red shift of 20 nm compared to the native state, a 5 % increase in ANS-fluorescence intensity relative to the native due to the surfacing of hydrophobic clusters and a sharp decrease in near-UV CD signal at around 284 and 291 nm. The state retains substantial native-like secondary structure. This partially unfolded intermediate state can be referred as 'molten globule', which finally tends to aggregate on day 6 and 4 with 50 and 100 mM glucose concentration, respectively, as a result of cross-linking between lysozyme molecules. The aggregates were confirmed by the presence of β-sheet structure as depicted by far-UV CD, an increase in ThT fluorescence as well as the fibrillar morphology shown by SEM. Moreover, advanced glycation end products were also accompanied as the emission peak was observed at 460 and 470 nm corresponding to the formation of pentosidine and malonaldehyde, respectively.
Collapse
|
20
|
Zárate-Romero A, Stojanoff V, Rojas-Trejo SP, Hansberg W, Rudiño-Piñera E. Conformational stability and crystal packing: polymorphism in Neurospora crassa CAT-3. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:753-8. [PMID: 23832201 DOI: 10.1107/s1744309113013468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/16/2013] [Indexed: 11/10/2022]
Abstract
Polymorphism is frequently observed from different crystallization conditions. In proteins, the effect on conformational variability is poorly documented, with only a few reported examples. Here, three polymorphic crystal structures determined for a large-subunit catalase, CAT-3 from Neurospora crassa, are reported. Two of them belonged to new space groups, P1 and P43212, and a third structure belonged to the same space group, P212121, as the previously deposited 2.3 Å resolution structure (PDB entry 3ej6), but had a higher resolution (1.95 Å). Comparisons between these polymorphic structures highlight the conformational stability of tetrameric CAT-3 and reveal a distortion in the tetrameric structure that has not previously been described.
Collapse
Affiliation(s)
- Andrés Zárate-Romero
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, MOR, Mexico.
| | | | | | | | | |
Collapse
|
21
|
Pattanayak SK, Chowdhuri S. Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
22
|
Salvador-Morales C, Valencia PM, Gao W, Karnik R, Farokhzad OC. Spontaneous formation of heterogeneous patches on polymer-lipid core-shell particle surfaces during self-assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:511-7. [PMID: 23109494 PMCID: PMC4157734 DOI: 10.1002/smll.201201499] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/29/2012] [Indexed: 05/27/2023]
Abstract
Spontaneous formation of heterogeneous patches on the surface of lipid-based nanoparticles (NPs) and microparticles (MPs) due to the segregation of two different functional groups. Patch formation is observed when tracing the functional groups with quantum dots, gold nanoparticles, and fluorescent dyes. This discovery could have important implications for the future design of self-assembled NPs and MPs for different biomedical applications.
Collapse
Affiliation(s)
- Carolina Salvador-Morales
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women’s Hospital-Harvard Medical School, Boston, MA 02115, USA
| | - Pedro M. Valencia
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Weiwei Gao
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women’s Hospital-Harvard Medical School, Boston, MA 02115, USA
| | - Rohit Karnik
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Omid C. Farokhzad
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women’s Hospital-Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
23
|
Cugia F, Monduzzi M, Ninham BW, Salis A. Interplay of ion specificity, pH and buffers: insights from electrophoretic mobility and pH measurements of lysozyme solutions. RSC Adv 2013. [DOI: 10.1039/c3ra00063j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
24
|
Li J, Bian H, Wen X, Chen H, Yuan K, Zheng J. Probing ion/molecule interactions in aqueous solutions with vibrational energy transfer. J Phys Chem B 2012; 116:12284-94. [PMID: 22984821 DOI: 10.1021/jp306369w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Interactions between model molecules representing building blocks of proteins and the thiocyanate anion, a strong protein denaturant agent, were investigated in aqueous solutions with intermolecular vibrational energy exchange methods. It was found that thiocyanate anions are able to bind to the charged ammonium groups of amino acids in aqueous solutions. The interactions between thiocyanate anions and the amide groups were also observed. The binding affinity between the thiocyanate anion and the charged amino acid residues is about 20 times larger than that between water molecules and the amino acids and about 5-10 times larger than that between the thiocyanate anion and the neutral backbone amide groups. The series of experiments also demonstrates that the chemical nature, rather than the macroscopic dielectric constant, of the ions and molecules plays a critical role in ion/molecule interactions in aqueous solutions.
Collapse
Affiliation(s)
- Jiebo Li
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | | | | | | | | | | |
Collapse
|
25
|
Chen H, Bian H, Li J, Wen X, Zheng J. Ultrafast multiple-mode multiple-dimensional vibrational spectroscopy. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.733116] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
26
|
Collins KD. Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions. Biophys Chem 2012; 167:43-59. [DOI: 10.1016/j.bpc.2012.04.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 01/13/2023]
|
27
|
Krause ME, Martin TT, Laurence JS. Mapping site-specific changes that affect stability of the N-terminal domain of calmodulin. Mol Pharm 2012; 9:734-43. [PMID: 22309490 DOI: 10.1021/mp2004109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biophysical tools have been invaluable in formulating therapeutic proteins. These tools characterize protein stability rapidly in a variety of solution conditions, but in general, the techniques lack the ability to discern site-specific information to probe how solution environment acts to stabilize or destabilize the protein. NMR spectroscopy can provide site-specific information about subtle structural changes of a protein under different conditions, enabling one to assess the mechanism of protein stabilization. In this study, NMR was employed to detect structural perturbations at individual residues as a result of altering pH and ionic strength. The N-terminal domain of calmodulin (N-CaM) was used as a model system, and the ¹H-¹⁵N heteronuclear single quantum coherence (HSQC) experiment was used to investigate effects of pH and ionic strength on individual residues. NMR analysis revealed that different solution conditions affect individual residues differently, even when the amino acid sequence and structure are highly similar. This study shows that addition of NMR to the formulation toolbox has the ability to extend understanding of the relationship between site-specific changes and overall protein stability.
Collapse
Affiliation(s)
- Mary E Krause
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
| | | | | |
Collapse
|
28
|
Pattanayak SK, Chowdhuri S. Effect of Water on Solvation Structure and Dynamics of Ions in the Peptide Bond Environment: Importance of Hydrogen Bonding and Dynamics of the Solvents. J Phys Chem B 2011; 115:13241-52. [DOI: 10.1021/jp206027e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751013, India
| |
Collapse
|
29
|
Gokarn YR, Fesinmeyer RM, Saluja A, Razinkov V, Chase SF, Laue TM, Brems DN. Effective charge measurements reveal selective and preferential accumulation of anions, but not cations, at the protein surface in dilute salt solutions. Protein Sci 2011; 20:580-7. [PMID: 21432935 DOI: 10.1002/pro.591] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Specific-ion effects are ubiquitous in nature; however, their underlying mechanisms remain elusive. Although Hofmeister-ion effects on proteins are observed at higher (>0.3 M) salt concentrations, in dilute (<0.1 M) salt solutions nonspecific electrostatic screening is considered to be dominant. Here, using effective charge (Q*) measurements of hen-egg white lysozyme (HEWL) as a direct and differential measure of ion-association, we experimentally show that anions selectively and preferentially accumulate at the protein surface even at low (<100 mM) salt concentrations. At a given ion normality (50 mN), the HEWL Q* was dependent on anion, but not cation (Li(+), Na(+), K(+), Rb(+), Cs(+), GdnH(+), and Ca(2+)), identity. The Q* decreased in the order F(-) > Cl(-) > Br(-) > NO(3)(-) ∼ I(-) > SCN(-) > ClO(4)(-) ≫ SO(4)(2-), demonstrating progressively greater binding of the monovalent anions to HEWL and also show that the SO(4)(2-) anion, despite being strongly hydrated, interacts directly with the HEWL surface. Under our experimental conditions, we observe a remarkable asymmetry between anions and cations in their interactions with the HEWL surface.
Collapse
Affiliation(s)
- Yatin R Gokarn
- Process and Product Development, Amgen Inc. Seattle, Washington 98119, USA.
| | | | | | | | | | | | | |
Collapse
|
30
|
Babin V, Roland C, Sagui C. The α-sheet: A missing-in-action secondary structure? Proteins 2011; 79:937-46. [DOI: 10.1002/prot.22935] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 10/26/2010] [Accepted: 10/28/2010] [Indexed: 11/06/2022]
|
31
|
Pozharski E. Percentile-based spread: a more accurate way to compare crystallographic models. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:970-8. [PMID: 20823548 DOI: 10.1107/s0907444910027927] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 07/13/2010] [Indexed: 11/10/2022]
Abstract
The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.
Collapse
|
32
|
Jones MJ, Ulrich J. Are Different Protein Crystal Modifications Polymorphs? A Discussion. Chem Eng Technol 2010. [DOI: 10.1002/ceat.201000148] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
33
|
Bončina M, Lah J, Reščič J, Vlachy V. Thermodynamics of the Lysozyme−Salt Interaction from Calorimetric Titrations. J Phys Chem B 2010; 114:4313-9. [DOI: 10.1021/jp9071845] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
34
|
Heyda J, Vincent JC, Tobias DJ, Dzubiella J, Jungwirth P. Ion Specificity at the Peptide Bond: Molecular Dynamics Simulations of N-Methylacetamide in Aqueous Salt Solutions. J Phys Chem B 2009; 114:1213-20. [DOI: 10.1021/jp910953w] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Heyda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Jordan C. Vincent
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Douglas J. Tobias
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Joachim Dzubiella
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| |
Collapse
|
35
|
Zhang Y, Cremer PS. The inverse and direct Hofmeister series for lysozyme. Proc Natl Acad Sci U S A 2009; 106:15249-53. [PMID: 19706429 PMCID: PMC2741236 DOI: 10.1073/pnas.0907616106] [Citation(s) in RCA: 311] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Indexed: 11/18/2022] Open
Abstract
Anion effects on the cloud-point temperature for the liquid-liquid phase transition of lysozyme were investigated by temperature gradient microfluidics under a dark field microscope. It was found that protein aggregation in salt solutions followed 2 distinct Hofmeister series depending on salt concentration. Namely, under low salt conditions the association of anions with the positively charged lysozyme surface dominated the process and the phase transition temperature followed an inverse Hofmeister series. This inverse series could be directly correlated to the size and hydration thermodynamics of the anions. At higher salt concentrations, the liquid-liquid phase transition displayed a direct Hofmeister series that correlated with the polarizability of the anions. A simple model was derived to take both charge screening and surface tension effects into account at the protein/water interface. Fitting the thermodynamic data to this model equation demonstrated its validity in both the high and low salt regimes. These results suggest that in general positively charged macromolecular systems should show inverse Hofmeister behavior only at relatively low salt concentrations, but revert to a direct Hofmeister series as the salt concentration is increased.
Collapse
Affiliation(s)
- Yanjie Zhang
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Paul S. Cremer
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| |
Collapse
|
36
|
Chruszcz M, Zimmerman MD, Wang S, Koclega KD, Zheng H, Evdokimova E, Kudritska M, Cymborowski M, Savchenko A, Edwards A, Minor W. Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1. CRYSTAL GROWTH & DESIGN 2008; 8:4054-4061. [PMID: 19898606 PMCID: PMC2700756 DOI: 10.1021/cg800430f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The crystal structure of PA5185, a putative thioesterase from Pseudomonas aeruginosa strain PAO1, was solved using multi-wavelength anomalous diffraction to 2.4 Å. Analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. The crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative PA5185 substrate (CoA or its derivative). Using new crystallization conditions containing this function-biased set of additives, several new crystal forms were produced and structures of three of them (in three different space groups) were determined. One of the new crystal forms had an improved resolution limit of 1.9 Å, and another displayed an alternative conformation of the highly-conserved loop containing Asn26, which could play a physiological role. Surprisingly, none of the additives were ordered in the crystal structures. Application of function-biased additives could be used as a standard optimization protocol for producing improved diffraction, or new crystal forms, which may lead to better understanding of the biological functions of proteins.
Collapse
Affiliation(s)
- Maksymilian Chruszcz
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Matthew D. Zimmerman
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Shuren Wang
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Katarzyna D. Koclega
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Heping Zheng
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Elena Evdokimova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Marina Kudritska
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Marcin Cymborowski
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Wladek Minor
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| |
Collapse
|
37
|
Protein crystal's shape and polymorphism prediction within the limits resulting from the exploration of the Miyazawa-Jernigan matrix. Biosystems 2008; 94:233-41. [PMID: 18721848 DOI: 10.1016/j.biosystems.2008.05.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Accepted: 05/30/2008] [Indexed: 11/24/2022]
Abstract
A computer study of the prediction of the protein crystal's shape and polymorphism of crystal's structures within the limits resulting from the exploration of the Miyazawa-Jernigan matrix is presented. In this study, a coarse-graining procedure was applied to prepare a two-dimensional growth unit, where instead of full atom representation of the protein a two-type (hydrophobic-hydrophilic, HP) aminoacidal representation was used. The interaction energies between hydrophobic (E(HH)) aminoacids were chosen from the well-known HP-type models (E(HH)in[-4,-3,-2.3,-1]), whereas interaction energies between hydrophobic and hydrophilic aminoacids (E(HP)) as well as interaction energies between hydrophilic aminoacids (E(PP)) were chosen from the range: <-1,1>, but not all values from this range fulfiled limitations resulting from the exploration of the Miyazawa-Jernigan matrix. Exploring every positively vetted combinations of energy interactions a polymorphism of the unit cell was observed what led to the fact that different final crystal's shapes were obtained.
Collapse
|
38
|
Pompidor G, D'Aléo A, Vicat J, Toupet L, Giraud N, Kahn R, Maury O. Protein Crystallography through Supramolecular Interactions between a Lanthanide Complex and Arginine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704683] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
39
|
Pompidor G, D'Aléo A, Vicat J, Toupet L, Giraud N, Kahn R, Maury O. Protein Crystallography through Supramolecular Interactions between a Lanthanide Complex and Arginine. Angew Chem Int Ed Engl 2008; 47:3388-91. [PMID: 18350532 DOI: 10.1002/anie.200704683] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Guillaume Pompidor
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075 CEA-CNRS-UJF-PSB, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | | | | | | | | | | | | |
Collapse
|
40
|
Tadeo X, Castaño D, Millet O. Anion modulation of the 1H/2H exchange rates in backbone amide protons monitored by NMR spectroscopy. Protein Sci 2007; 16:2733-40. [PMID: 17965190 DOI: 10.1110/ps.073027007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The ability of three anionic cosolutes (sulfate, thiocyanate, and chloride) in modulating the (1)H/(2)H exchange rates for backbone amide protons has been investigated using nuclear magnetic resonance (NMR) for two different proteins: the IGg-binding domain of protein L (ProtL) and the glucose-galactose-binding protein (GGBP). Our results show that moderate anion concentrations (0.2 M-1 M) regulate the exchange rate following the Hofmeister series: Addition of thiocyanate increases the exchange rates for both proteins, while sulfate and chloride (to a less extent) slow down the exchange reaction. In the presence of the salt, no alteration of the protein structure and minimal variations in the number of measurable peaks are observed. Experiments with model compounds revealed that the unfolded state is modulated in an equivalent way by these cosolutes. For ProtL, the estimated values for the local free energy change upon salt addition (m (3,DeltaG )) are consistent with the previously reported free energy contribution from the cosolute's preferential interaction/exclusion term indicating that nonspecific weak interactions between the anion and the amide groups constitute the dominant mechanism for the exchange-rate modulation. The same trend is also found for GGBP in the presence of thiocyanate, underlining the generality of the exchange-rate modulation mechanism, complementary to more investigated effects like the electrostatic interactions or specific anion binding to protein sites.
Collapse
Affiliation(s)
- Xavier Tadeo
- Structural Biology Unit, CIC bioGUNE, 48160 Derio, Spain
| | | | | |
Collapse
|
41
|
Benvenuti M, Mangani S. Crystallization of soluble proteins in vapor diffusion for x-ray crystallography. Nat Protoc 2007; 2:1633-51. [PMID: 17641629 DOI: 10.1038/nprot.2007.198] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The preparation of protein single crystals represents one of the major obstacles in obtaining the detailed 3D structure of a biological macromolecule. The complete automation of the crystallization procedures requires large investments in terms of money and labor, which are available only to large dedicated infrastructures and is mostly suited for genomic-scale projects. On the other hand, many research projects from departmental laboratories are devoted to the study of few specific proteins. Here, we try to provide a series of protocols for the crystallization of soluble proteins, especially the difficult ones, tailored for small-scale research groups. An estimate of the time needed to complete each of the steps described can be found at the end of each section.
Collapse
Affiliation(s)
- Manuela Benvenuti
- Dipartimento di Chimica, Università di Siena, Via Aldo Moro 2, Siena 53100, Italy
| | | |
Collapse
|
42
|
|
43
|
Abstract
A novel secondary structure, the alpha-sheet, was identified through molecular dynamics (MD) simulations of various proteins associated with amyloid diseases under amyloidogenic conditions. The structure was first predicted by Pauling and Corey, and it has been directly observed in crystal structures of "nonnatural peptides". There are occurrences of alpha-strands and alpha-sheets in the Protein Data Bank, but they are rare. We propose that alpha-sheet is formed during the conformational changes associated with amyloidosis and that it may represent the toxic conformer. Here, structural properties of the alpha-sheet, background information, and experimental support for this novel structure are presented. Finally we speculate about the possible role of this conformation in disease.
Collapse
Affiliation(s)
- Valerie Daggett
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, USA
| |
Collapse
|
44
|
Povey JF, Smales CM, Hassard SJ, Howard MJ. Comparison of the effects of 2,2,2-trifluoroethanol on peptide and protein structure and function. J Struct Biol 2006; 157:329-38. [PMID: 16979904 DOI: 10.1016/j.jsb.2006.07.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 07/20/2006] [Accepted: 07/22/2006] [Indexed: 10/24/2022]
Abstract
The co-solvent 2,2,2-trifluoroethanol (TFE) has been often used to aid formation of secondary structure in solution peptides or alternately as a denaturant within protein folding studies. Hen egg white lysozyme (HEWL) and a synthetic model peptide defining HEWL helix-4 were used as comparative model systems to systematically investigate the effect of increasing TFE concentrations on the structure of proteins and peptides. HEWL was analyzed using NMR, far-UV CD and fluorescence spectroscopy; with correlation of these results towards changes in enzymatic activity and the helix-4 peptide was analysed using NMR. Data illustrates two conflicting modes of interaction: Low TFE concentrations stabilize tertiary structure, observed from an increase in the number of NMR NOE contacts. Higher TFE concentrations denatured HEWL with the loss of lysozyme tertiary structure. The effects of TFE upon secondary structural elements within HEWL are distinct from those observed for the helix-4 peptide. This illustrates a dissimilar interaction of TFE towards both protein and peptide at equivalent TFE concentrations. The concentration that TFE promotes stabilization over denaturation is likely to be protein dependent although the structural action can be extrapolated to other protein systems with implications for the use of TFE in structural stability studies.
Collapse
Affiliation(s)
- Jane F Povey
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | | | | | | |
Collapse
|
45
|
Vergara A, Lorber B, Sauter C, Giegé R, Zagari A. Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology. Biophys Chem 2005; 118:102-12. [PMID: 16150532 DOI: 10.1016/j.bpc.2005.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 06/23/2005] [Accepted: 06/23/2005] [Indexed: 11/24/2022]
Abstract
The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.
Collapse
Affiliation(s)
- Alessandro Vergara
- Dipartimento di Chimica, Università di Napoli Federico II, Monte S. Angelo, 80126, Napoli, Italia
| | | | | | | | | |
Collapse
|
46
|
Poznański J, Wszelaka-Rylik M, Zielenkiewicz W. HEW lysozyme salting by high-concentration NaCl solutions followed by titration calorimetry. Biophys Chem 2005; 113:137-44. [PMID: 15617820 DOI: 10.1016/j.bpc.2004.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 08/31/2004] [Indexed: 11/19/2022]
Abstract
Concentration dependence of NaCl salting of 0-1.5 mM lysozyme solution in 0.1 M sodium acetate buffer, pH 4.25, was investigated for NaCl concentration varying up to 0.9 M. Calorimetric experiments demonstrated that depending on the salt concentration the estimated number of the binding sites on the lysozyme surface varied in the range of 5 up to 13, and the increase of salt concentration caused the decrease of the number of accessible sites. The small, but significant, local maximum centered at 0.63 M NaCl concentration indicated the specific salting-out of the lysozyme accompanied by binding of approximately 2-3 chloride anions. Generalized McMillan and Mayer's approach reduced to the third-order virial coefficients demonstrates the domination of lysozyme aggregation upon salt addition (a(21)-h(xxy)) and salt organization on the lysozyme surface (a(12)-h(xyy)) processes.
Collapse
Affiliation(s)
- Jarosław Poznański
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | | | | |
Collapse
|
47
|
Li SJ, Nakagawa A, Tsukihara T. Ni2+ binds to active site of hen egg-white lysozyme and quenches fluorescence of Trp62 and Trp108. Biochem Biophys Res Commun 2004; 324:529-33. [PMID: 15474459 DOI: 10.1016/j.bbrc.2004.09.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Indexed: 11/30/2022]
Abstract
We found that the maximum emission of the tryptophyl fluorescence of hen egg-white lysozyme is shifted from 337 to 323 nm and quenched to the extent of 55% with an increase in concentrations of NiCl2 from 0 to 2M in 50 mM Na acetate buffer (pH 4.7). In contrast, NaCl does not influence the fluorescence of lysozyme up to 2M. To elucidate the particular effects of Ni2+ on the tryptophyl fluorescence of lysozyme, we have measured the assembly behavior and secondary structure of lysozyme in various concentrations of NiCl2, and determined the structures of lysozyme crystals grown in 0.3, 0.5, and 1.0M NiCl2, respectively. The results of analytical centrifugation and circular dichroism experiments show that lysozyme keeps a monomer state and has an identical secondary structure, irrespective of NiCl2 concentrations. The crystal structures show that all crystals grown in different concentrations of NiCl2 have an identical main chain and side chain conformation. And one Ni2+ binding with Odelta atom of Asp52 in the active site and coordinating with five water molecules to form hexagonal coordination has been determined for each crystal structure. Based on these results, we have proposed that Ni2+ quenches the fluorescence of Trp62 and Trp108 due to the binding of Ni2+ to the active site of lysozyme.
Collapse
Affiliation(s)
- Shu Jie Li
- Division of Protein Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | | | | |
Collapse
|
48
|
Bernadó P, Blackledge M. Anisotropic small amplitude Peptide plane dynamics in proteins from residual dipolar couplings. J Am Chem Soc 2004; 126:4907-20. [PMID: 15080696 DOI: 10.1021/ja036977w] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of small amplitude anisotropic peptide plane motion on residual dipolar couplings (RDC) measured in proteins has been investigated. RDC averaging effects in the presence of GAF (Gaussian axial fluctuation) motions are found to vary strongly depending on the peptide plane orientation. Even low amplitude dynamics can significantly affect derived alignment tensor parameters if this motion is not taken into account. An analytical description of averaged N-(N)H RDCs is introduced that includes basic GAF-like motion. The averaging depends on the orientation of the peptide plane (alpha, beta, gamma) in the alignment frame and on the motional amplitude (sigma). This expression is used to investigate the presence of anisotropic reorientational dynamics in proteins by incorporating sigma as an additional parameter into the alignment tensor analysis. Average GAF amplitudes (sigma(av)) are determined for secondary structural elements from single experimental N-(N)H RDC data sets from five different proteins, in combination with high-resolution structural models. This yields statistically significant improvement over the static description, and detects sigma(av) values ranging from 14.4 to 17.0 degrees for the different proteins. A higher value of sigma(av) = 20 degrees from loop regions was found using two independent sets of N-(N)H RDC in the protein lysozyme, for which a very high-resolution structure is available. Comparison of fitting behavior over 13 structures from lysozyme of crystal diffraction resolution ranging from 0.9 to 2.1A indicates a small spread of motional amplitudes, demonstrating that the method is robust up to this level of resolution. A combined definition of (alpha)C-C' and N-(N)H RDC under the influence of GAF motions allows simultaneous fitting of both RDC. Application to three proteins leads to similar sigma(av) values and a more significant improvement with respect to the static model. Using the GAF model to describe conformationally averaged RDC is important for two reasons: a more accurate definition of the alignment tensor magnitude can be derived, and the method can be used to detect average small amplitude motions in protein backbones from readily accessible data, on time scales not easily sampled by other NMR techniques.
Collapse
Affiliation(s)
- Pau Bernadó
- Institut de Biologie Structurale Jean-Pierre Ebel, UJF-CNRS-CEA, 41 rue Jules Horowitz, 38027 Grenoble Cedex, France
| | | |
Collapse
|
49
|
Majeed S, Ofek G, Belachew A, Huang CC, Zhou T, Kwong PD. Enhancing protein crystallization through precipitant synergy. Structure 2003; 11:1061-70. [PMID: 12962625 DOI: 10.1016/s0969-2126(03)00185-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Suitable conditions for protein crystallization are commonly identified by screening combinations of independent factors that affect crystal formation. Because precipitating agents are prime determinants of crystallization, we investigated whether a systematic exploration of combinations of mechanistically distinct precipitants would enhance crystallization. A crystallization screen containing 64 precipitant mixtures was devised. Tests with ten HIV envelope-related proteins demonstrated that use of precipitant mixtures significantly enhanced both the probability of crystallization as well as the quality of optimized crystals. Tests with hen egg white lysozyme generated a novel C2 crystal from a salt/organic solvent mixture; structure solution at 2 A resolution revealed a lattice held together by both hydrophobic and electrostatic dyad interactions. The results indicate that mechanistically distinct precipitants can synergize, with precipitant combinations adding unique dimensions to protein crystallization.
Collapse
Affiliation(s)
- Shahzad Majeed
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | |
Collapse
|
50
|
Mason PE, Neilson GW, Dempsey CE, Barnes AC, Cruickshank JM. The hydration structure of guanidinium and thiocyanate ions: implications for protein stability in aqueous solution. Proc Natl Acad Sci U S A 2003; 100:4557-61. [PMID: 12684536 PMCID: PMC404697 DOI: 10.1073/pnas.0735920100] [Citation(s) in RCA: 276] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neutron diffraction experiments were carried out on aqueous solutions containing either guanidinium or thiocyanate ions. The first-order difference method of neutron diffraction and isotopic substitution was applied, and the hydration structures of two of nature's strongest denaturant ions were determined. Each ion is shown to interact weakly with water: Guanidinium has no recognizable hydration shell and is one of the most weakly hydrated cations yet characterized. Hydration of thiocyanate is characterized by a low coordination number involving around one hydrogen-bonded water molecule and approximately two water molecules weakly interacting through "hydration bonds." The weak hydration of these denaturant ions strongly supports suggestions that a major contribution to the denaturant effect is the preferential interaction of the denaturant with the protein surface. By contrast, solute species such as many sugars and related polyols that stabilize proteins are strongly hydrated and are thus preferentially retained in the bulk solvent and excluded from the protein surface.
Collapse
Affiliation(s)
- P E Mason
- Department of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | | | | | | | | |
Collapse
|