1
|
Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
Collapse
Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| |
Collapse
|
2
|
Roeters SJ, Mertig R, Lutz H, Roehrich A, Drobny G, Weidner T. Backbone Structure of Diatom Silaffin Peptide R5 in Biosilica Determined by Combining Solid-State NMR with Theoretical Sum-Frequency Generation Spectra. J Phys Chem Lett 2021; 12:9657-9661. [PMID: 34586816 DOI: 10.1021/acs.jpclett.1c02786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Silaffin peptide R5 is key for the biogenesis of silica cell walls of diatoms. Biosilification by the R5 peptide has potential in biotechnology, drug development, and materials science due to its ability to precipitate stable, high fidelity silica sheets and particles. A true barrier for the design of novel peptide-based architectures for wider applications has been the limited understanding of the interfacial structure of R5 when precipitating silica nanoparticles. While R5-silica interactions have been studied in detail at flat surfaces, the structure within nanophase particles is still being debated. We herein elucidate the conformation of R5 in its active form within silica particles by combining interface-specific vibrational spectroscopy data with solid-state NMR torsion angles using theoretical spectra. Our calculations show that R5 is structured and undergoes a conformational transition from a strand-type motif in solution to a more curved, contracted structure when interacting with silica precursors.
Collapse
Affiliation(s)
- Steven J Roeters
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Rolf Mertig
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Helmut Lutz
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| |
Collapse
|
3
|
Bialas F, Reichinger D, Becker CF. Biomimetic and biopolymer-based enzyme encapsulation. Enzyme Microb Technol 2021; 150:109864. [DOI: 10.1016/j.enzmictec.2021.109864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/02/2021] [Accepted: 06/29/2021] [Indexed: 12/25/2022]
|
4
|
Weidner T, Castner DG. Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:389-412. [PMID: 33979545 PMCID: PMC8522203 DOI: 10.1146/annurev-anchem-091520-010206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.
Collapse
Affiliation(s)
- Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark;
| | - David G Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Departments of Bioengineering and Chemical Engineering, University of Washington, Seattle, Washington 98195, USA;
| |
Collapse
|
5
|
Manning JH, Walkley B, Provis JL, Patwardhan SV. Mimicking Biosintering: The Identification of Highly Condensed Surfaces in Bioinspired Silica Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:561-568. [PMID: 33372796 PMCID: PMC7815198 DOI: 10.1021/acs.langmuir.0c03261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Interfacial interactions between inorganic surfaces and organic additives are vital to develop new complex nanomaterials. Learning from biosilica materials, composite nanostructures have been developed, which exploit the strength and directionality of specific polyamine additive-silica surface interactions. Previous interpretations of these interactions are almost universally based on interfacial charge matching and/or hydrogen bonding. In this study, we analyzed the surface chemistry of bioinspired silica (BIS) materials using solid-state nuclear magnetic resonance (NMR) spectroscopy as a function of the organic additive concentration. We found significant additional association between the additives and fully condensed (Q4) silicon species compared to industrial silica materials, leading to more overall Q4 concentration and higher hydrothermal stability, despite BIS having a shorter synthesis time. We posit that the polyfunctionality and catalytic activity of additives in the BIS synthesis lead to both of these surface phenomena, contrasting previous studies on monofunctional surfactants used in most other artificial templated silica syntheses. From this, we propose that additive polyfunctionality can be used to generate tailored artificial surfaces in situ and provide insights into the process of biosintering in biosilica systems, highlighting the need for more in-depth simulations on interfacial interactions at silica surfaces.
Collapse
Affiliation(s)
- Joseph
R. H. Manning
- Department
of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, U.K.
- Department
of Chemical Engineering, The University
of Bath, Bath BA2 7AY, U.K.
- Department
of Chemistry, University College London, London WC1E 6BT, U.K.
| | - Brant Walkley
- Department
of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, U.K.
- Department
of Materials Science and Engineering, The
University of Sheffield, Sheffield S1 3JD, U.K.
| | - John L. Provis
- Department
of Materials Science and Engineering, The
University of Sheffield, Sheffield S1 3JD, U.K.
| | - Siddharth V. Patwardhan
- Department
of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, U.K.
| |
Collapse
|
6
|
Shaw WJ, Tarasevich BJ, Buchko GW, Arachchige RMJ, Burton SD. Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite. J Struct Biol 2020; 212:107630. [PMID: 32979496 PMCID: PMC7744360 DOI: 10.1016/j.jsb.2020.107630] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.
Collapse
Affiliation(s)
- Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Barbara J Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Bioscience, Washington State University, Pullman, WA 99164, USA
| | - Rajith M J Arachchige
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah D Burton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| |
Collapse
|
7
|
Iline-Vul T, Nanda R, Mateos B, Hazan S, Matlahov I, Perelshtein I, Keinan-Adamsky K, Althoff-Ospelt G, Konrat R, Goobes G. Osteopontin regulates biomimetic calcium phosphate crystallization from disordered mineral layers covering apatite crystallites. Sci Rep 2020; 10:15722. [PMID: 32973201 PMCID: PMC7518277 DOI: 10.1038/s41598-020-72786-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
Details of apatite formation and development in bone below the nanometer scale remain enigmatic. Regulation of mineralization was shown to be governed by the activity of non-collagenous proteins with many bone diseases stemming from improper activity of these proteins. Apatite crystal growth inhibition or enhancement is thought to involve direct interaction of these proteins with exposed faces of apatite crystals. However, experimental evidence of the molecular binding events that occur and that allow these proteins to exert their functions are lacking. Moreover, recent high-resolution measurements of apatite crystallites in bone have shown that individual crystallites are covered by a persistent layer of amorphous calcium phosphate. It is therefore unclear whether non-collagenous proteins can interact with the faces of the mineral crystallites directly and what are the consequences of the presence of a disordered mineral layer to their functionality. In this work, the regulatory effect of recombinant osteopontin on biomimetic apatite is shown to produce platelet-shaped apatite crystallites with disordered layers coating them. The protein is also shown to regulate the content and properties of the disordered mineral phase (and sublayers within it). Through solid-state NMR atomic carbon-phosphorous distance measurements, the protein is shown to be located in the disordered phases, reaching out to interact with the surfaces of the crystals only through very few sidechains. These observations suggest that non-phosphorylated osteopontin acts as regulator of the coating mineral layers and exerts its effect on apatite crystal growth processes mostly from afar with a limited number of contact points with the crystal.
Collapse
Affiliation(s)
- Taly Iline-Vul
- Department of Chemistry, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Raju Nanda
- Department of Chemistry, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Borja Mateos
- Max F. Perutz Laboratories, Department of Computational and Structural Biology, University of Vienna, 1030, Vienna, Austria
| | - Shani Hazan
- Department of Chemistry, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Irina Matlahov
- Department of Chemistry, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Ilana Perelshtein
- Department of Chemistry, Bar Ilan University, 5290002, Ramat Gan, Israel
| | | | | | - Robert Konrat
- Max F. Perutz Laboratories, Department of Computational and Structural Biology, University of Vienna, 1030, Vienna, Austria
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, 5290002, Ramat Gan, Israel.
| |
Collapse
|
8
|
Wang X, Yang X, Chen H, Yang X, Xu Z. Entropy-Enthalpy Compensation in Peptide Adsorption on Solid Surfaces: Dependence on Surface Hydration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10822-10829. [PMID: 32813538 DOI: 10.1021/acs.langmuir.0c01845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although protein adsorption at the solid-water interface is of immense importance, understanding the crucial role of the water phase in mediating protein-surface interactions is lacking, particularly due to the lack of fundamental thermodynamic data. Herein, we have performed complicated free energy calculations and successfully extracted the entropy and enthalpy changes of molecular adsorption on solids. Using the gold and graphene as the surface models with distinct affinities to the water phase, we successfully unravel the sharply opposite manners of entropy-enthalpy compensation in driving water and tripeptide adsorptions on two surfaces. Though the thermodynamic features of water adsorption on surface are enthalpically dominated based on the positions of free energy barriers and minima, the favorable entropy term significantly decreases the free energy barrier and further stabilizes the adsorbate at the adsorption site on the graphene surface. For the peptide, the shape of the adsorption free energy profile is jointly determined by the enthalpy and entropy changes, which, however, alternatively act the driving force to promote the peptide adsorption on the Au surface and graphene surface. The distinct structural and dynamic properties of solid-liquid interfaces account for the special role of the interfacial water phase in regulating the competitive relationship between the entropy and enthalpy variations.
Collapse
Affiliation(s)
- Xiang Wang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Huijun Chen
- Obstetrics and Gynecology Department, Zhongnan Hospital of Wuhan University, #169 East Lake Road, Wuchang District, Wuhan 430017, China
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
- Zhangjiagang Institute of Nanjing Tech University, Jiangfanlu 8, Zhangjiagang 215699, China
| |
Collapse
|
9
|
Dračínský M, Vícha J, Bártová K, Hodgkinson P. Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids. Chemphyschem 2020; 21:2075-2083. [PMID: 32691463 DOI: 10.1002/cphc.202000629] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH2 , CH3 , OH, SH and NH3 ) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.
Collapse
Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic
| | - Jan Vícha
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic.,Centre of Polymer Systems, Tomas Bata University in Zlín, Tomáše Bati 5678, Zlín, CZ-760 01, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
| |
Collapse
|
10
|
Ping H, Poudel L, Xie H, Fang W, Zou Z, Zhai P, Wagermaier W, Fratzl P, Wang W, Wang H, O'Reilly P, Ching WY, Fu Z. Synthesis of monodisperse rod-shaped silica particles through biotemplating of surface-functionalized bacteria. NANOSCALE 2020; 12:8732-8741. [PMID: 32307501 DOI: 10.1039/d0nr00669f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mesoporous silica particles of controlled size and shape are potentially beneficial for many applications, but their usage may be limited by the complex procedure of fabrication. Biotemplating provides a facile approach to synthesize materials with desired shapes. Herein, a bioinspired design principle is adopted through displaying silaffin-derived 5R5 proteins on the surface of Escherichia coli by genetic manipulations. The genetically modified Escherichia coli provides a three-dimensional template to regulate the synthesis of rod-shaped silica. The silicification is initiated on the cell surface under the functionality of 5R5 proteins and subsequentially the inner space is gradually filled. Density functional theory simulation reveals the interfacial interactions between silica precursors and R5 peptides at the atomic scale. There is a large conformation change of this protein during biosilicification. Electrostatic interactions contribute to the high affinity between positively charged residues (Lys4, Arg16, Arg17) and negatively charged tetraethyl orthosilicate. Hydrogen bonds develop between Arg16 (OH), Arg17 (OH and NH), Leu19 (OH) residues and the forming silica agglomerates. In addition, the resulting rod-shaped silica copy of the bacteria can transform into mesoporous SiOx nanorods composed of carbon-coated nanoparticles after carbonization, which is shown to allow superior lithium storage performance.
Collapse
Affiliation(s)
- Hang Ping
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, 430070, China.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Kolbe F, Daus F, Geyer A, Brunner E. Phosphate-Silica Interactions in Diatom Biosilica and Synthetic Composites Studied by Rotational Echo Double Resonance (REDOR) NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4332-4338. [PMID: 32233513 DOI: 10.1021/acs.langmuir.0c00336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biosilica is a biogenic composite material produced by organisms like diatoms. Various biomolecules are tightly attached or incorporated into biosilica. Examples are special proteins termed silaffins and long-chain polyamines (LCPAs). Presumably, these biomolecules are involved in the biosilica formation process. Silaffins are highly phosphorylated zwitterions with LCPAs post-translationally attached to lysine residues. In the present work, we use distance-dependent solid-state NMR experiments, especially the 31P{29Si} Rotational Echo Double Resonance (REDOR) technique, to study the environment of phosphate moieties in biosilica and in vitro synthesized SiO2-based composites. In contrast to the heterogeneous mixtures of biomolecules found in native biosilica, the described in vitro silicification experiments make use of a single synthetic phosphopeptide and an LCPA of well-defined and uniform structure. The heteronuclear correlations measured from these silica composites provide reliable 31P-29Si dipolar second moments and information about the distribution of the phosphopeptide within the silica material. The calculated second moment indicates close contact between phosphopeptides and silica. The phosphopeptides are incorporated into the silica composite in a disperse manner. Moreover, the REDOR data acquired for diatom biosilica also imply that phosphate groups are part of the silica-organic interface in this material.
Collapse
Affiliation(s)
- Felicitas Kolbe
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Fabian Daus
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Eike Brunner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| |
Collapse
|
12
|
Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| |
Collapse
|
13
|
Olmez TT, Sahin Kehribar E, Isilak ME, Lu TK, Seker UOS. Synthetic Genetic Circuits for Self-Actuated Cellular Nanomaterial Fabrication Devices. ACS Synth Biol 2019; 8:2152-2162. [PMID: 31419103 DOI: 10.1021/acssynbio.9b00235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genetically controlled synthetic biosystems are being developed to create nanoscale materials. These biosystems are modeled on the natural ability of living cells to synthesize materials: many organisms have dedicated proteins that synthesize a wide range of hard tissues and solid materials, such as nanomagnets and biosilica. We designed an autonomous living material synthesizing system consisting of engineered cells with genetic circuits that synthesize nanomaterials. The circuits encode a nanomaterial precursor-sensing module (sensor) coupled with a materials synthesis module. The sensor detects the presence of cadmium, gold, or iron ions, and this detection triggers the synthesis of the related nanomaterial-nucleating extracellular matrix. We demonstrate that when engineered cells sense the availability of a precursor ion, they express the corresponding extracellular matrix to form the nanomaterials. This proof-of-concept study shows that endowing cells with synthetic genetic circuits enables nanomaterial synthesis and has the potential to be extended to the synthesis of a variety of nanomaterials and biomaterials using a green approach.
Collapse
Affiliation(s)
- Tolga Tarkan Olmez
- UNAM- Institute of Materials and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Ebru Sahin Kehribar
- UNAM- Institute of Materials and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Musa Efe Isilak
- UNAM- Institute of Materials and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Timothy K. Lu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | | |
Collapse
|
14
|
Malmberg P, Norén JG, Bernin D. Molecular insights into hypomineralized enamel. Eur J Oral Sci 2019; 127:340-346. [DOI: 10.1111/eos.12619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Per Malmberg
- Department of Chemistry and Chemical Engineering Chalmers University of Technology Gothenburg Sweden
| | - Jörgen G. Norén
- Department of Pediatric Dentistry Institute of Odontology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Diana Bernin
- Department of Chemistry and Chemical Engineering Chalmers University of Technology Gothenburg Sweden
- Swedish NMR Centre University of Gothenburg Gothenburg Sweden
| |
Collapse
|
15
|
Buckle EL, Prakash A, Bonomi M, Sampath J, Pfaendtner J, Drobny GP. Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces. J Am Chem Soc 2019; 141:1998-2011. [PMID: 30618247 PMCID: PMC6785181 DOI: 10.1021/jacs.8b10990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Elucidation of the structure and interactions of proteins at native mineral interfaces is key to understanding how biological systems regulate the formation of hard tissue structures. In addition, understanding how these same proteins interact with non-native mineral surfaces has important implications for the design of medical and dental implants, chromatographic supports, diagnostic tools, and a host of other applications. Here, we combine solid-state NMR spectroscopy, isotherm measurements, and molecular dynamics simulations to study how SNa15, a peptide derived from the hydroxyapatite (HAP) recognition domain of the biomineralization protein statherin, interacts with HAP, silica (SiO2), and titania (TiO2) mineral surfaces. Adsorption isotherms are used to characterize the binding affinity of SNa15 to HAP, SiO2, and TiO2. We also apply 1D 13C CP MAS, 1D 15N CP MAS, and 2D 13C-13C DARR experiments to SNa15 samples with uniformly 13C- and 15N-enriched residues to determine backbone and side-chain chemical shifts. Different computational tools, namely TALOS-N and molecular dynamics simulations, are used to deduce secondary structure from backbone and side-chain chemical shift data. Our results show that SNa15 adopts an α-helical conformation when adsorbed to HAP and TiO2, but the helix largely unravels upon adsorption to SiO2. Interactions with HAP are mediated in general by acidic and some basic amino acids, although the specific amino acids involved in direct surface interaction vary with surface. The integrated experimental and computational approach used in this study is able to provide high-resolution insights into adsorption of proteins on interfaces.
Collapse
Affiliation(s)
- Erika L. Buckle
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Arushi Prakash
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, 75015 Paris, France
| | - Janani Sampath
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Gary P. Drobny
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| |
Collapse
|
16
|
Xu Z, Yang X, Wei Q, Zhao W, Cui B, Yang X, Sahai N. Quantitatively Identifying the Roles of Interfacial Water and Solid Surface in Governing Peptide Adsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7932-7941. [PMID: 29888924 DOI: 10.1021/acs.langmuir.8b01189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the molecular mechanism of protein adsorption on solids is critical to their applications in materials synthesis and tissue engineering. Although the water phase at the surface/water interface has been recognized as three types: bulk water, intermediate water phase and surface-bound water layers, the roles of the water and surface in determining the protein adsorption are not clearly identified, particularly at the quantitative level. Herein, we provide a methodology involving the combination of microsecond strengthen sampling simulation and force integration to quantitatively characterize the water-induced contribution and the peptide-surface interactions into the adsorption free energy. Using hydroxyapatite and graphene surfaces as examples, we demonstrate how the distinct interfacial features dominate the delicate force balance between these two thermodynamics parameters, leading to surface preference/resistance to peptide adsorption. Specifically, the water layer provides sustained repelling force against peptide adsorption, as indicated by a monotonic increase in the water-induced free energy profile, whereas the contribution from the surface-peptide interactions is thermodynamically favorable to peptide adsorptions. More importantly, the revealed adsorption mechanism is critically dictated by the distribution of water phase, which plays a crucial role in establishing the force balance between the interactions of the peptide with the water layer and the surface. For the HAP surface, the charged peptide exhibits strong binding affinity to the surface, due to the controlling contribution of peptide-surface interaction in the intermediate water phase. The surface-bound water layers are observed as the origin of bioresistance of solid surfaces toward the adsorption of charge-neutral peptides. The preferred peptide adsorption on the graphene, however, is dominated by the surface-induced component at the water layers adjacent to the surface. Our results further elucidate that the intermediate water phase significantly shortens the effective range of the surface dispersion force, in contrast to the observation on the hydrophilic surface.
Collapse
Affiliation(s)
| | | | | | - Weilong Zhao
- Department of Polymer Science , University of Akron , Akron , Ohio 44325-3909 , United States
| | | | | | - Nita Sahai
- Department of Polymer Science , University of Akron , Akron , Ohio 44325-3909 , United States
| |
Collapse
|
17
|
Buckle EL, Lum JS, Roehrich AM, Stote RE, Vandermoon B, Dracinsky M, Filocamo SF, Drobny GP. Serine-Lysine Peptides as Mediators for the Production of Titanium Dioxide: Investigating the Effects of Primary and Secondary Structures Using Solid-State NMR Spectroscopy and DFT Calculations. J Phys Chem B 2018; 122:4708-4718. [PMID: 29595262 DOI: 10.1021/acs.jpcb.8b00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A biomimetic approach to the formation of titania (TiO2) nanostructures is desirable because of the mild conditions required in this form of production. We have identified a series of serine-lysine peptides as candidates for the biomimetic production of TiO2 nanostructures. We have assayed these peptides for TiO2-precipitating activity upon exposure to titanium bis(ammonium lactato)dihydroxide and have characterized the resulting coprecipitates using scanning electron microscopy. A subset of these assayed peptides efficiently facilitates the production of TiO2 nanospheres. Here, we investigate the process of TiO2 nanosphere formation mediated by the S-K peptides KSSKK- and SKSK3SKS using one-dimensional and two-dimensional solid-state NMR (ssNMR) on peptide samples with uniformly 13C-enriched residues. ssNMR is used to assign 13C chemical shifts (CSs) site-specifically in each free peptide and TiO2-embedded peptide, which are used to derive secondary structures in the neat and TiO2 coprecipitated states. The backbone 13C CSs are used to assess secondary structural changes undergone during the coprecipitation process. Side-chain 13C CS changes are analyzed with density functional theory calculations and used to determine side-chain conformational changes that occur upon coprecipitation with TiO2 and to determine surface orientation of lysine side chains in TiO2-peptide composites.
Collapse
Affiliation(s)
- Erika L Buckle
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| | - June S Lum
- Biological Sciences and Technology Team , US Army Natick Soldier Research, Development and Engineering Center , Natick , Massachusetts 01760 , United States
| | - Adrienne M Roehrich
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| | - Robert E Stote
- Biological Sciences and Technology Team , US Army Natick Soldier Research, Development and Engineering Center , Natick , Massachusetts 01760 , United States
| | - Branden Vandermoon
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| | - Martin Dracinsky
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo 2 , 16610 Prague , Czech Republic
| | - Shaun F Filocamo
- Biological Sciences and Technology Team , US Army Natick Soldier Research, Development and Engineering Center , Natick , Massachusetts 01760 , United States
| | - Gary P Drobny
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| |
Collapse
|
18
|
Vowinkel S, Paul S, Gutmann T, Gallei M. Free-Standing and Self-Crosslinkable Hybrid Films by Core-Shell Particle Design and Processing. NANOMATERIALS (BASEL, SWITZERLAND) 2017; 7:E390. [PMID: 29140279 PMCID: PMC5707607 DOI: 10.3390/nano7110390] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022]
Abstract
The utilization and preparation of functional hybrid films for optical sensing applications and membranes is of utmost importance. In this work, we report the convenient and scalable preparation of self-crosslinking particle-based films derived by directed self-assembly of alkoxysilane-based cross-linkers as part of a core-shell particle architecture. The synthesis of well-designed monodisperse core-shell particles by emulsion polymerization is the basic prerequisite for subsequent particle processing via the melt-shear organization technique. In more detail, the core particles consist of polystyrene (PS) or poly(methyl methacrylate) (PMMA), while the comparably soft particle shell consists of poly(ethyl acrylate) (PEA) and different alkoxysilane-based poly(methacrylate)s. For hybrid film formation and convenient self-cross-linking, different alkyl groups at the siloxane moieties were investigated in detail by solid-state Magic-Angle Spinning Nuclear Magnetic Resonance (MAS, NMR) spectroscopy revealing different crosslinking capabilities, which strongly influence the properties of the core or shell particle films with respect to transparency and iridescent reflection colors. Furthermore, solid-state NMR spectroscopy and investigation of the thermal properties by differential scanning calorimetry (DSC) measurements allow for insights into the cross-linking capabilities prior to and after synthesis, as well as after the thermally and pressure-induced processing steps. Subsequently, free-standing and self-crosslinked particle-based films featuring excellent particle order are obtained by application of the melt-shear organization technique, as shown by microscopy (TEM, SEM).
Collapse
Affiliation(s)
- Steffen Vowinkel
- Ernst-Berl-Institute for Chemical Engineering and Macromolecular Science, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, D-64287 Darmstadt, Germany.
| | - Stephen Paul
- Eduard-Zintl Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287 Darmstadt, Germany.
| | - Torsten Gutmann
- Eduard-Zintl Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287 Darmstadt, Germany.
| | - Markus Gallei
- Ernst-Berl-Institute for Chemical Engineering and Macromolecular Science, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, D-64287 Darmstadt, Germany.
| |
Collapse
|
19
|
Zerfaß C, Buchko GW, Shaw WJ, Hobe S, Paulsen H. Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P 5 S 3 during silicic acid condensation and silica decondensation. Proteins 2017; 85:2111-2126. [PMID: 28799215 PMCID: PMC5760248 DOI: 10.1002/prot.25366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/08/2022]
Abstract
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.
Collapse
Affiliation(s)
- Christian Zerfaß
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Garry W. Buchko
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Stephan Hobe
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| |
Collapse
|
20
|
Buckle EL, Roehrich A, Vandermoon B, Drobny GP. Comparative Study of Secondary Structure and Interactions of the R5 Peptide in Silicon Oxide and Titanium Oxide Coprecipitates Using Solid-State NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10517-10524. [PMID: 28898103 PMCID: PMC6786483 DOI: 10.1021/acs.langmuir.7b01048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A biomimetic, peptide-mediated approach to inorganic nanostructure formation is of great interest as an alternative to industrial production methods. To investigate the role of peptide structure on silica (SiO2) and titania (TiO2) morphologies, we use the R5 peptide domain derived from the silaffin protein to produce uniform SiO2 and TiO2 nanostructures from the precursor silicic acid and titanium bis(ammonium lactato)dihydroxide, respectively. The resulting biosilica and biotitania nanostructures are characterized using scanning electron microscopy. To investigate the process of R5-mediated SiO2 and TiO2 formation, we carry out 1D and 2D solid-state NMR (ssNMR) studies on R5 samples with uniformly 13C- and 15N-labeled residues to determine the backbone and side-chain chemical shifts. 13C chemical shift data are in turn used to determine peptide backbone torsion angles and secondary structure for the R5 peptide neat, in silica, and in titania. We are thus able to assess the impact of the different mineral environments on peptide structure, and we can further elucidate from 13C chemical shifts change the degree to which various side chains are in close proximity to the mineral phases. These comparisons add to the understanding of the role of R5 and its structure in both SiO2 and TiO2 formation.
Collapse
Affiliation(s)
- Erika L Buckle
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Branden Vandermoon
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| |
Collapse
|
21
|
Cerofolini L, Giuntini S, Louka A, Ravera E, Fragai M, Luchinat C. High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix. J Phys Chem B 2017; 121:8094-8101. [PMID: 28762736 DOI: 10.1021/acs.jpcb.7b05679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.
Collapse
Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.,GiottoBiotech S.R.L. , Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| |
Collapse
|
22
|
Lutz H, Jaeger V, Schmüser L, Bonn M, Pfaendtner J, Weidner T. The Structure of the Diatom Silaffin Peptide R5 within Freestanding Two-Dimensional Biosilica Sheets. Angew Chem Int Ed Engl 2017; 56:8277-8280. [DOI: 10.1002/anie.201702707] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Helmut Lutz
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Vance Jaeger
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Lars Schmüser
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Jim Pfaendtner
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Tobias Weidner
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| |
Collapse
|
23
|
Lutz H, Jaeger V, Schmüser L, Bonn M, Pfaendtner J, Weidner T. Die Struktur des Silaffin-Peptids R5 aus Diatomeen in freistehenden zweidimensionalen Biosilikatwänden. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Helmut Lutz
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Vance Jaeger
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Lars Schmüser
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Jim Pfaendtner
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Tobias Weidner
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Dänemark
| |
Collapse
|
24
|
Adiram-Filiba N, Schremer A, Ohaion E, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Goobes G. Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization. Biointerphases 2017; 12:02D414. [PMID: 28565916 PMCID: PMC5451314 DOI: 10.1116/1.4983273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/16/2022] Open
Abstract
Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.
Collapse
Affiliation(s)
| | - Avital Schremer
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Ohaion
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| |
Collapse
|
25
|
Brückner SI, Donets S, Dianat A, Bobeth M, Gutiérrez R, Cuniberti G, Brunner E. Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:11698-11705. [PMID: 27759396 DOI: 10.1021/acs.langmuir.6b03311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively 13C-labeled choline with 29Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like 1H-13C CP-REDOR (rotational-echo double resonance), 1H-13C HETCOR (heteronuclear correlation), and 1H-29Si-1H double CP are employed to determine spatial parameters. The measurement of 29Si-13C internuclear distances for selectively 13C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.
Collapse
Affiliation(s)
- Stephan Ingmar Brückner
- Chair for Bioanalytical Chemistry, Department of Chemistry and Food Chemistry, TU Dresden , 01062 Dresden, Germany
| | - Sergii Donets
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden , 01062 Dresden, Germany
| | - Arezoo Dianat
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden , 01062 Dresden, Germany
| | - Manfred Bobeth
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden , 01062 Dresden, Germany
| | - Rafael Gutiérrez
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden , 01062 Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden , 01062 Dresden, Germany
- Dresden Center for Computational Materials Science (DCMS), TU Dresden , 01062 Dresden, Germany
- Center for Advancing Electronics Dresden, TU Dresden , 01062 Dresden, Germany
| | - Eike Brunner
- Chair for Bioanalytical Chemistry, Department of Chemistry and Food Chemistry, TU Dresden , 01062 Dresden, Germany
| |
Collapse
|
26
|
Li Y, Reid DG, Bazin D, Daudon M, Duer MJ. Solid state NMR of salivary calculi: Proline-rich salivary proteins, citrate, polysaccharides, lipids, and organic–mineral interactions. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
27
|
Ravera E, Martelli T, Geiger Y, Fragai M, Goobes G, Luchinat C. Biosilica and bioinspired silica studied by solid-state NMR. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
28
|
Zhao W, Xu Z, Cui Q, Sahai N. Predicting the Structure-Activity Relationship of Hydroxyapatite-Binding Peptides by Enhanced-Sampling Molecular Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7009-7022. [PMID: 27329793 DOI: 10.1021/acs.langmuir.6b01582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the molecular structural and energetic basis of the interactions between peptides and inorganic surfaces is critical to their applications in tissue engineering and biomimetic material synthesis. Despite recent experimental progresses in the identification and functionalization of hydroxyapatite (HAP)-binding peptides, the molecular mechanisms of their interactions with HAP surfaces are yet to be explored. In particular, the traditional method of molecular dynamics (MD) simulation suffers from insufficient sampling at the peptide-inorganic interface that renders the molecular-level observation dubious. Here we demonstrate that an integrated approach combining bioinformatics, MD, and metadynamics provides a powerful tool for investigating the structure-activity relationship of HAP-binding peptides. Four low charge density peptides, previously identified by phage display, have been considered. As revealed by bioinformatics and MD, the binding conformation of the peptides is controlled by both the sequence and the amino acid composition. It was found that formation of hydrogen bonds between lysine residue and phosphate ions on the surface dictates the binding of positively charged peptide to HAP. The binding affinities of the peptides to the surface are estimated by free energy calculation using parallel-tempering metadynamics, and the results compare favorably to measurements reported in previous experimental studies. The calculation suggests that the charge density of the peptide primarily controls the binding affinity to the surface, while the backbone secondary structure that may restrain side chain orientation toward the surface plays a minor role. We also report that the application of enhanced-sampling metadynamics effects a major advantage over the steered MD method by significantly improving the reliability of binding free energy calculation. In general, our novel integration of diverse sampling techniques should contribute to the rational design of surface-recognition peptides in biomedical applications.
Collapse
Affiliation(s)
| | | | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , Madison, Wisconsin 53706-1322, United States
| | | |
Collapse
|
29
|
Ravera E, Cerofolini L, Martelli T, Louka A, Fragai M, Luchinat C. (1)H-detected solid-state NMR of proteins entrapped in bioinspired silica: a new tool for biomaterials characterization. Sci Rep 2016; 6:27851. [PMID: 27279168 PMCID: PMC4899708 DOI: 10.1038/srep27851] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/24/2016] [Indexed: 01/16/2023] Open
Abstract
Proton-detection in solid-state NMR, enabled by high magnetic fields (>18 T) and fast magic angle spinning (>50 kHz), allows for the acquisition of traditional (1)H-(15)N experiments on systems that are too big to be observed in solution. Among those, proteins entrapped in a bioinspired silica matrix are an attractive target that is receiving a large share of attention. We demonstrate that (1)H-detected SSNMR provides a novel approach to the rapid assessment of structural integrity in proteins entrapped in bioinspired silica.
Collapse
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Tommaso Martelli
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| |
Collapse
|
30
|
Geiger Y, Gottlieb HE, Akbey Ü, Oschkinat H, Goobes G. Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR. J Am Chem Soc 2016; 138:5561-7. [DOI: 10.1021/jacs.5b07809] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasmin Geiger
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Hugo E. Gottlieb
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ümit Akbey
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert-Roessle-Str.
10, Berlin 13125, Germany
| | - Hartmut Oschkinat
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert-Roessle-Str.
10, Berlin 13125, Germany
| | - Gil Goobes
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| |
Collapse
|
31
|
Smith AN, Long JR. Dynamic Nuclear Polarization as an Enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2016; 88:122-32. [PMID: 26594903 PMCID: PMC5704910 DOI: 10.1021/acs.analchem.5b04376] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Adam N Smith
- Department of Chemistry, University of Florida , 214 Leigh Hall, Gainesville, Florida 32611-7200, United States
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, University of Florida , P. O. Box 100245, Gainesville, Florida 32610-0245, United States
| |
Collapse
|
32
|
Martelli T, Ravera E, Louka A, Cerofolini L, Hafner M, Fragai M, Becker CFW, Luchinat C. Atomic-Level Quality Assessment of Enzymes Encapsulated in Bioinspired Silica. Chemistry 2015; 22:425-32. [DOI: 10.1002/chem.201503613] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/23/2022]
|
33
|
Jantschke A, Koers E, Mance D, Weingarth M, Brunner E, Baldus M. Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:15069-73. [DOI: 10.1002/anie.201507327] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 01/23/2023]
|
34
|
Jantschke A, Koers E, Mance D, Weingarth M, Brunner E, Baldus M. Einblick in die supramolekulare Architektur von intaktem Diatomeen-Biosilikat mithilfe DNP-verstärkter Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
35
|
Ravera E, Michaelis VK, Ong TC, Keeler EG, Martelli T, Fragai M, Griffin RG, Luchinat C. Biosilica-Entrapped Enzymes Studied by Using Dynamic Nuclear-Polarization-Enhanced High-Field NMR Spectroscopy. Chemphyschem 2015; 16:2751-2754. [PMID: 26266832 PMCID: PMC4752418 DOI: 10.1002/cphc.201500549] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 11/08/2022]
Abstract
Enzymes are used as environmentally friendly catalysts in many industrial applications, and are frequently immobilized in a matrix to improve their chemical stability for long-term storage and reusability. Recently, it was shown that an atomic-level description of proteins immobilized in a biosilica matrix can be attained by examining their magic-angle spinning (MAS) NMR spectra. However, even though MAS NMR is an excellent tool for determining structure, it is severely hampered by sensitivity. In this work we provide the proof of principle that NMR characterization of biosilica-entrapped enzymes could be assisted by high-field dynamic nuclear polarization (DNP).
Collapse
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Vladimir K. Michaelis
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ta-Chung Ong
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eric G. Keeler
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tommaso Martelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| |
Collapse
|
36
|
Shaw WJ. Solid-state NMR studies of proteins immobilized on inorganic surfaces. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 70:1-14. [PMID: 25466354 PMCID: PMC4615564 DOI: 10.1016/j.ssnmr.2014.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/14/2014] [Accepted: 10/16/2014] [Indexed: 05/23/2023]
Abstract
Solid state NMR is the primary tool for studying the quantitative, site-specific structure, orientation, and dynamics of biomineralization proteins under biologically relevant conditions. Two calcium phosphate proteins, statherin (43 amino acids) and leucine rich amelogenin protein (LRAP; 59 amino acids), have been studied in depth and have different dynamic properties and 2D- and 3D-structural features. These differences make it difficult to extract design principles used in nature for building materials with properties such as high strength, unusual morphologies, or uncommon phases. Consequently, design principles needed for developing synthetic materials controlled by proteins are not clear. Many biomineralization proteins are much larger than statherin and LRAP, necessitating the study of larger biomineralization proteins. More recent studies of the significantly larger full-length amelogenin (180 residues) represent a significant step forward to ultimately investigate the full diversity of biomineralization proteins. Interactions of amino acids, a silaffin derived peptide, and the model LK peptide with silica are also being studied, along with qualitative studies of the organic matrices interacting with calcium carbonate. Dipolar recoupling techniques have formed the core of the quantitative studies, yet the need for isolated spin pairs makes this approach costly and time intensive. The use of multi-dimensional techniques to study biomineralization proteins is becoming more common, methodology which, despite its challenges with these difficult-to-study proteins, will continue to drive future advancements in this area.
Collapse
Affiliation(s)
- Wendy J Shaw
- Pacific Northwest National Laboratory, PO Box 999, MS K2-57, Richland, WA 99352, USA.
| |
Collapse
|
37
|
Ravera E, Fragai M, Parigi G, Luchinat C. Differences in Dynamics between Crosslinked and Non-Crosslinked Hyaluronates Measured by using Fast Field-Cycling Relaxometry. Chemphyschem 2015; 16:2803-2809. [PMID: 26263906 DOI: 10.1002/cphc.201500446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 11/11/2022]
Abstract
The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid-state NMR spectroscopy, and scanning electron microscopy. A model-free analysis of field-dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.
Collapse
Affiliation(s)
- Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Marco Fragai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Giacomo Parigi
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Claudio Luchinat
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| |
Collapse
|
38
|
Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
Collapse
Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| |
Collapse
|
39
|
Experimental characterization of adsorbed protein orientation, conformation, and bioactivity. Biointerphases 2015; 10:019002. [PMID: 25708632 DOI: 10.1116/1.4906485] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Protein adsorption on material surfaces is a common phenomenon that is of critical importance in many biotechnological applications. The structure and function of adsorbed proteins are tightly interrelated and play a key role in the communication and interaction of the adsorbed proteins with the surrounding environment. Because the bioactive state of a protein on a surface is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary dataset to characterize and understand the bioactive state of adsorbed protein. Over the past several years, the authors have focused on the development of such a set of complementary methods to address this need. These methods include adsorbed-state circular dichroism spectropolarimetry to determine adsorption-induced changes in protein secondary structure, amino-acid labeling/mass spectrometry to assess adsorbed protein orientation and tertiary structure by monitoring adsorption-induced changes in residue solvent accessibility, and bioactivity assays to assess adsorption-induced changes in protein bioactivity. In this paper, the authors describe the methods that they have developed and/or adapted for each of these assays. The authors then provide an example of their application to characterize how adsorption-induced changes in protein structure influence the enzymatic activity of hen egg-white lysozyme on fused silica glass, high density polyethylene, and poly(methyl-methacrylate) as a set of model systems.
Collapse
|
40
|
Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective. J Phys Chem B 2015; 119:2857-68. [PMID: 25594631 DOI: 10.1021/jp511386b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deuterium line shape analysis of CD3 groups has emerged as a particularly useful tool for studying microsecond-millisecond protein motions in the solid state. The models devised so far consist of several independently conceived simple jump-type motions. They are comprised of physical quantities encoded in their simplest form; improvements are only possible by adding yet another simple motion, thereby changing the model. The various treatments developed are case-specific; hence comparison among the different systems is not possible. Here we develop a new methodology for (2)H NMR line shape analysis free of these limitations. It is based on the microscopic-order-macroscopic-disorder (MOMD) approach. In MOMD motions are described by diffusion tensors, spatial restrictions by potentials/ordering tensors, and geometric features by relative tensor orientations. Jump-type motions are recovered in the limit of large orientational potentials. Model improvement is accomplished by monitoring the magnitude, symmetry, and orientation of the various tensors. The generality of MOMD makes possible comparison among different scenarios. CD3 line shapes from the Chicken Villin Headpiece Subdomain and the Streptomyces Subtilisin Inhibitor are used as experimental examples. All of these spectra are reproduced by using rhombic local potentials constrained for simplicity to be given by the L = 2 spherical harmonics, and by axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2-3 k(B)T. The diffusion tensor is tilted at 120° from the C-CD3 axis. The perpendicular (parallel) correlation times for local motion are 0.1-1.0 ms (3.3-30 μs). Activation energies in the 1.1-8.0 kcal/mol range are estimated. Future prospects include extension to the (2)H relaxation limit, application to the (15)N and (13)C NMR nuclei, and accounting for collective motions and anisotropic media.
Collapse
Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
| | | | | |
Collapse
|
41
|
Senior L, Crump MP, Williams C, Booth PJ, Mann S, Perriman AW, Curnow P. Structure and function of the silicifying peptide R5. J Mater Chem B 2015; 3:2607-2614. [DOI: 10.1039/c4tb01679c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first detailed description of the structure and function of the silicifying peptide R5.
Collapse
Affiliation(s)
- Laura Senior
- School of Biochemistry
- University of Bristol
- UK
- Bristol Centre for Functional Nanomaterials
- University of Bristol
| | | | | | | | | | - Adam W. Perriman
- School of Cellular and Molecular Medicine
- University of Bristol
- UK
| | - Paul Curnow
- School of Biochemistry
- University of Bristol
- UK
| |
Collapse
|
42
|
Zane AC, Michelet C, Roehrich A, Emani PS, Drobny GP. Silica morphogenesis by lysine-leucine peptides with hydrophobic periodicity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7152-7161. [PMID: 24896500 DOI: 10.1021/la501444t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The use of biomimetic approaches in the production of inorganic nanostructures is of great interest to the scientific and industrial community due to the relatively moderate physical conditions needed. In this vein, taking cues from silaffin proteins used by unicellular diatoms, several studies have identified peptide candidates for the production of silica nanostructures. In the current article, we study intensively one such silica-precipitating peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), an amphiphilic lysine/leucine repeat peptide that self-organizes into an α-helical secondary structure under appropriate concentration and buffer conditions. The suggested mechanism of precipitation is that the sequestration of hydrophilic lysines on one side of this helix allows interaction with the negatively charged surface of silica nanoparticles, which in turn can aggregate further into larger structures. To investigate the process, we carry out 1D and 2D solid-state NMR (ssNMR) studies on samples with one or two uniformly (13)C- and (15)N-labeled residues to determine the backbone and side-chain chemical shifts. We also further study the dynamics of two leucine residues in the sequence through (13)C spin-lattice relaxation times (T1) to determine the impact of silica coprecipitation on their mobility. Our results confirm the α-helical secondary structure in both the neat and silica-complexed states of the peptide, and the patterns of chemical shift and relaxation time changes between the two states suggest possible mechanisms of self-aggregation and silica precipitation.
Collapse
Affiliation(s)
- Ariel C Zane
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | | | | | | | | |
Collapse
|
43
|
Solid-state NMR studies of metal-free SOD1 fibrillar structures. J Biol Inorg Chem 2014; 19:659-66. [PMID: 24719206 DOI: 10.1007/s00775-014-1130-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Copper-zinc superoxide dismutase 1 (SOD1) is present in the protein aggregates deposited in motor neurons of amyotrophic lateral sclerosis (ALS) patients. ALS is a neurodegenerative disease that can be either sporadic (ca. 90%) or familial (fALS). The most widely studied forms of fALS are caused by mutations in the sequence of SOD1. Ex mortuo SOD1 aggregates are usually found to be amorphous. In vitro SOD1, in its immature reduced and apo state, forms fibrillar aggregates. Previous literature data have suggested that a monomeric SOD1 construct, lacking loops IV and VII, (apoSODΔIV-VII), shares the same fibrillization properties of apoSOD1, both proteins having the common structural feature of the central β-barrel. In this work, we show that structural information can be obtained at a site-specific level from solid-state NMR. The residues that are sequentially assignable are found to be located at the putative nucleation site for fibrillar species formation in apoSOD, as detected by other experimental techniques.
Collapse
|
44
|
Goobes G. Past and Future Solid-State NMR Spectroscopy Studies at the Convergence Point between Biology and Materials Research. Isr J Chem 2014. [DOI: 10.1002/ijch.201300113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
45
|
Fragai M, Luchinat C, Martelli T, Ravera E, Sagi I, Solomonov I, Udi Y. SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation in atomic detail. Chem Commun (Camb) 2014; 50:421-3. [DOI: 10.1039/c3cc46896h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Ferella L, Luchinat C, Ravera E, Rosato A. SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR. JOURNAL OF BIOMOLECULAR NMR 2013; 57:319-26. [PMID: 24243317 DOI: 10.1007/s10858-013-9795-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/11/2013] [Indexed: 05/09/2023]
Abstract
We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.
Collapse
Affiliation(s)
- Lucio Ferella
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | | | | | | |
Collapse
|