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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.
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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.
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2
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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.
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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
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3
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Hellner B, Alamdari S, Pyles H, Zhang S, Prakash A, Sprenger KG, De Yoreo JJ, Baker D, Pfaendtner J, Baneyx F. Sequence–Structure–Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study. J Am Chem Soc 2020; 142:2355-2363. [DOI: 10.1021/jacs.9b11617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | - Shuai Zhang
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | | | - James J. De Yoreo
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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4
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Emani PS, Yimer YY, Davidowski SK, Gebhart RN, Ferreira HE, Kuprov I, Pfaendtner J, Drobny GP. Combining Molecular and Spin Dynamics Simulations with Solid-State NMR: A Case Study of Amphiphilic Lysine-Leucine Repeat Peptide Aggregates. J Phys Chem B 2019; 123:10915-10929. [PMID: 31769684 DOI: 10.1021/acs.jpcb.9b09245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state nuclear magnetic resonance (ssNMR) data to elucidate molecular dynamics (MD) involves modeling the restriction to overall tumbling by neighbors, as well as the concentrations of water and buffer. In this exploration of the factors that influence motion, we utilize atomistic MD trajectories of peptide aggregates with varying hydration to mimic an amorphous solid-state environment and predict ssNMR relaxation rates. We also account for spin diffusion in multiply spin-labeled (up to 19 nuclei) residues, with several models of dipolar-coupling networks. The framework serves as a general approach to determine essential spin couplings affecting relaxation, benchmark MD force fields, and reveal the hydration dependence of dynamics in a crowded environment. We demonstrate the methodology on a previously characterized amphiphilic 14-residue lysine-leucine repeat peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), which has an α-helical secondary structure and putatively forms leucine-burying tetramers in the solid state. We measure the R1 relaxation rates of uniformly 13C-labeled and site-specific 2H-labeled leucines in the hydrophobic core of LKα14 at multiple hydration levels. Studies of 9 and 18 tetramer bundles reveal the following: (a) for the incoherent component of 13C relaxation, the nearest-neighbor spin interactions dominate, while the 1H-1H interactions have minimal impact; (b) the AMBER ff14SB dihedral barriers for the leucine Cγ-Cδ bond ("methyl rotation barriers") must be lowered by a factor of 0.7 to better match the 2H data; (c) proton-driven spin diffusion explains some of the discrepancy between experimental and simulated rates for the Cβ and Cα nuclei; and (d) 13C relaxation rates are mostly underestimated in the MD simulations at all hydrations, and the discrepancies identify likely motions missing in the 50 ns MD trajectories.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Yeneneh Y Yimer
- Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States
| | - Stephen K Davidowski
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Rachel N Gebhart
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Helen E Ferreira
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Ilya Kuprov
- Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , U.K
| | - Jim Pfaendtner
- Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States
| | - Gary P Drobny
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
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5
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Sampath J, Pfaendtner J. Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1657192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Janani Sampath
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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Altintoprak K, Farajollahi F, Seidenstücker A, Ullrich T, Wenz NL, Krolla P, Plettl A, Ziemann P, Marti O, Walther P, Exner D, Schwaiger R, Gliemann H, Wege C. Improved manufacture of hybrid membranes with bionanopore adapters capable of self-luting. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2019. [DOI: 10.1680/jbibn.18.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Farid Farajollahi
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Timo Ullrich
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Peter Krolla
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Alfred Plettl
- Institute of Solid State Physics, University of Ulm, Ulm, Germany
| | - Paul Ziemann
- Institute of Solid State Physics, University of Ulm, Ulm, Germany
| | - Othmar Marti
- Institute of Experimental Physics, University of Ulm, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, University of Ulm, Ulm, Germany
| | - Daniela Exner
- Institute for Applied Materials – Materials and Biomechanics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Ruth Schwaiger
- Institute for Applied Materials – Materials and Biomechanics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Hartmut Gliemann
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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7
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Ndao M, Goobes G, Emani PS, Drobny GP. A REDOR ssNMR Investigation of the Role of an N-Terminus Lysine in R5 Silica Recognition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8678-8684. [PMID: 27039990 PMCID: PMC6785185 DOI: 10.1021/acs.langmuir.5b04114] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Diatoms are unicellular algae that construct cell walls called frustules by the precipitation of silica, using special proteins that order the silica into a wide variety of nanostructures. The diatom species Cylindrotheca fusiformis contains proteins called silaffins within its frustules, which are believed to assemble into supramolecular matrices that serve as both accelerators and templates for silica deposition. Studying the properties of these biosilicification proteins has allowed the design of new protein and peptide systems that generate customizable silica nanostructures, with potential generalization to other mineral systems. It is essential to understand the mechanisms of aggregation of the protein and its coprecipitation with silica. We continue previous investigations into the peptide R5, derived from silaffin protein sil1p, shown to independently catalyze the precipitation of silica nanospheres in vitro. We used the solid-state NMR technique 13C{29Si} and 15N{29Si} REDOR to investigate the structure and interactions of R5 in complex with coprecipitated silica. These experiments are sensitive to the strength of magnetic dipole-dipole interactions between the 13C nuclei in R5 and the 29Si nuclei in the silica and thus yield distance between parts of R5 and 29Si in silica. Our data show strong interactions and short internuclear distances of 3.74 ± 0.20 Å between 13C═O Lys3 and silica. On the other hand, the Cα and Cβ nuclei show little or no interaction with 29Si. This selective proximity between the K3 C═O and the silica supports a previously proposed mechanism of rapid silicification of the antimicrobial peptide KSL (KKVVFKVKFK) through an imidate intermediate. This study reports for the first time a direct interaction between the N-terminus of R5 and silica, leading us to believe that the N-terminus of R5 is a key component in the molecular recognition process and a major factor in silica morphogenesis.
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Affiliation(s)
- Moise Ndao
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Prashant S. Emani
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Gary P. Drobny
- Department of Chemistry, University of Washington, Seattle, WA 98195
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8
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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.
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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
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9
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Iline-Vul T, Adiram-Filiba N, Matlahov I, Geiger Y, Abayev M, Keinan-Adamsky K, Akbey U, Oschkinat H, Goobes G. Understanding the roles of functional peptides in designing apatite and silica nanomaterials biomimetically using NMR techniques. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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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.
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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
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11
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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.
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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
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12
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Ferreira HE, Drobny GP. Solid state deuterium NMR study of LKα14 peptide aggregation in biosilica. Biointerphases 2017; 12:02D418. [PMID: 28655279 PMCID: PMC5552403 DOI: 10.1116/1.4986907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/26/2017] [Accepted: 06/07/2017] [Indexed: 11/17/2022] Open
Abstract
In nature, organisms including diatoms, radiolaria, and marine sponges use proteins, long chain polyamines, and other organic molecules to regulate the assembly of complex silica-based structures. Here, the authors investigate structural features of small peptides, designed to mimic the silicifying activities of larger proteins found in natural systems. LKα14 (Ac-LKKLLKLLKKLLKL-C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, coprecipitates with silica to form nanospheres. Previous 13C magic angle spinning studies suggest that the tetrameric peptide bundles that LKα14 is known to form in solution may persist in the silica-complexed form, and may also function as catalysts and templates for silica formation. To further investigate LKα14 aggregation in silica, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how leucine side-chain dynamics differ in solid LKα14 peptides isolated from aqueous solution, from phosphate-buffered solution, and in the silica-precipitated states. Modeling the 2H ssNMR line shapes probed the mechanisms of peptide preaggregation and silica coprecipitation. The resulting NMR data indicates that the peptide bundles in silica preserve the hydrophobic interior that they display in the hydrated solid state. However, NMR data also indicate free motion of the leucine residues in silica, a condition that may result from structural deformation of the aggregates arising from interactions between the surface lysine side chains and the surrounding silica matrix.
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Affiliation(s)
- Helen E Ferreira
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Gary P Drobny
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
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13
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Palunas K, Sprenger K, Weidner T, Pfaendtner J. Effect of an ionic liquid/air Interface on the structure and dynamics of amphiphilic peptides. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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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.
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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
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15
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Lemloh ML, Altintoprak K, Wege C, Weiss IM, Rothenstein D. Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization. MATERIALS (BASEL, SWITZERLAND) 2017; 10:E119. [PMID: 28772478 PMCID: PMC5459154 DOI: 10.3390/ma10020119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022]
Abstract
Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO₂ mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.
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Affiliation(s)
- Marie-Louise Lemloh
- Institute of Biomaterials and Biomolecular Systems (IBBS), Biobased Materials, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Klara Altintoprak
- Institute of Biomaterials and Biomolecular Systems (IBBS), Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems (IBBS), Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
- Projekthaus NanoBioMater, Allmandring 5B, 70569 Stuttgart, Germany.
| | - Ingrid M Weiss
- Institute of Biomaterials and Biomolecular Systems (IBBS), Biobased Materials, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
- Projekthaus NanoBioMater, Allmandring 5B, 70569 Stuttgart, Germany.
| | - Dirk Rothenstein
- Projekthaus NanoBioMater, Allmandring 5B, 70569 Stuttgart, Germany.
- Institute for Materials Science, Chair of Chemical Materials Synthesis, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
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16
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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]
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17
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Sprenger KG, Pfaendtner J. Strong Electrostatic Interactions Lead to Entropically Favorable Binding of Peptides to Charged Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5690-5701. [PMID: 27181161 DOI: 10.1021/acs.langmuir.6b01296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Thermodynamic analyses can provide key insights into the origins of protein self-assembly on surfaces, protein function, and protein stability. However, obtaining quantitative measurements of thermodynamic observables from unbiased classical simulations of peptide or protein adsorption is challenging because of sampling limitations brought on by strong biomolecule/surface binding forces as well as time scale limitations. We used the parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) enhanced sampling method to study the adsorption behavior and thermodynamics of several explicitly solvated model peptide adsorption systems, providing new molecular-level insight into the biomolecule adsorption process. Specifically studied were peptides LKα14 and LKβ15 and trpcage miniprotein adsorbing onto a charged, hydrophilic self-assembled monolayer surface functionalized with a carboxylic acid/carboxylate headgroup and a neutral, hydrophobic methyl-terminated self-assembled monolayer surface. Binding free energies were calculated as a function of temperature for each system and decomposed into their respective energetic and entropic contributions. We investigated how specific interfacial features such as peptide/surface electrostatic interactions and surface-bound ion content affect the thermodynamic landscape of adsorption and lead to differences in surface-bound conformations of the peptides. Results show that upon adsorption to the charged surface, configurational entropy gains of the released solvent molecules dominate the configurational entropy losses of the bound peptide. This behavior leads to an apparent increase in overall system entropy upon binding and therefore to the surprising and seemingly nonphysical result of an apparent increased binding free energy at elevated temperatures. Opposite effects and conclusions are found for the neutral surface. Additional simulations demonstrate that by adjusting the ionic strength of the solution, results that show the expected physical behavior, i.e., peptide binding strength that decreases with increasing temperature or is independent of temperature altogether, can be recovered on the charged surface. On the basis of this analysis, an overall free energy for the entire thermodynamic cycle for peptide adsorption on charged surfaces is constructed and validated with independent simulations.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195-1750, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195-1750, United States
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18
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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
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19
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Jackson E, Ferrari M, Cuestas-Ayllon C, Fernández-Pacheco R, Perez-Carvajal J, de la Fuente JM, Grazú V, Betancor L. Protein-templated biomimetic silica nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3687-3695. [PMID: 25741589 DOI: 10.1021/la504978r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biomimetic silica particles can be synthesized as a nanosized material within minutes in a process mimicked from living organisms such as diatoms and sponges. In this work, we have studied the effect of bovine serum albumin (BSA) as a template to direct the synthesis of silica nanoparticles (NPs) with the potential to associate proteins on its surface. Our approach enables the formation of spheres with different physicochemical properties. Particles using BSA as a protein template were smaller (∼250-380 nm) and were more monodisperse than those lacking the proteic core (∼700-1000 nm) as seen by dynamic light scattering (DLS), scanning electron microscopy (SEM), and environmental scanning electron microscopy (ESEM) analysis. The absence of BSA during synthesis produced silica nanoparticles without any porosity that was detectable by nitrogen adsorption, whereas particles containing BSA developed porosity in the range of 4 to 5 nm which collapsed on the removal of BSA, thus producing smaller pores. These results were in accordance with the pore size calculated by high-resolution transmission electron microscopy (HTEM). The reproducibility of the BSA-templated nanoparticle properties was determined by analyzing four batches of independent synthesizing experiments that maintained their properties. The high positive superficial charge of the nanoparticles facilitated adsorption under mild conditions of a range of proteins from an E. coli extract and a commercial preparation of laccase from Trametes versicolor. All of the proteins were quantitatively desorbed. Experiments conducted showed the reusability of the particles as supports for the ionic adsorption of the biomolecules. The protein loading capacity of the BSA-based biomimetic particles was determined using laccase as 98.7 ± 6.6 mg·g(-1) of particles.
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Affiliation(s)
- Erienne Jackson
- †Laboratorio de Biotecnología, Facultad de Ingeniería-Universidad ORT Uruguay, 11100 Montevideo, Uruguay
| | - Mariana Ferrari
- †Laboratorio de Biotecnología, Facultad de Ingeniería-Universidad ORT Uruguay, 11100 Montevideo, Uruguay
| | - Carlos Cuestas-Ayllon
- ‡Instituto de Nanociencia de Aragon (INA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | | | - Javier Perez-Carvajal
- §Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz 3, Cantoblanco 28049 Madrid, Spain
| | - Jesús M de la Fuente
- ∥Instituto de Ciencia de Materiales de Aragón (ICMA), CSIC-Universidad de Zaragoza, c/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- ⊥Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of the Ministry of Education, Research Institute of Translation Medicine, Shanghai Jiao Tong University, Dongchuan Road 800, 200240 Shanghai, People's Republic of China
| | - Valeria Grazú
- ‡Instituto de Nanociencia de Aragon (INA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Lorena Betancor
- †Laboratorio de Biotecnología, Facultad de Ingeniería-Universidad ORT Uruguay, 11100 Montevideo, Uruguay
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20
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Altintoprak K, Seidenstücker A, Welle A, Eiben S, Atanasova P, Stitz N, Plettl A, Bill J, Gliemann H, Jeske H, Rothenstein D, Geiger F, Wege C. Peptide-equipped tobacco mosaic virus templates for selective and controllable biomineral deposition. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:1399-1412. [PMID: 26199844 PMCID: PMC4505087 DOI: 10.3762/bjnano.6.145] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/29/2015] [Indexed: 05/22/2023]
Abstract
The coating of regular-shaped, readily available nanorod biotemplates with inorganic compounds has attracted increasing interest during recent years. The goal is an effective, bioinspired fabrication of fiber-reinforced composites and robust, miniaturized technical devices. Major challenges in the synthesis of applicable mineralized nanorods lie in selectivity and adjustability of the inorganic material deposited on the biological, rod-shaped backbones, with respect to thickness and surface profile of the resulting coating, as well as the avoidance of aggregation into extended superstructures. Nanotubular tobacco mosaic virus (TMV) templates have proved particularly suitable towards this goal: Their multivalent protein coating can be modified by high-surface-density conjugation of peptides, inducing and governing silica deposition from precursor solutions in vitro. In this study, TMV has been equipped with mineralization-directing peptides designed to yield silica coatings in a reliable and predictable manner via precipitation from tetraethoxysilane (TEOS) precursors. Three peptide groups were compared regarding their influence on silica polymerization: (i) two peptide variants with alternating basic and acidic residues, i.e. lysine-aspartic acid (KD) x motifs expected to act as charge-relay systems promoting TEOS hydrolysis and silica polymerization; (ii) a tetrahistidine-exposing polypeptide (CA4H4) known to induce silicification due to the positive charge of its clustered imidazole side chains; and (iii) two peptides with high ZnO binding affinity. Differential effects on the mineralization of the TMV surface were demonstrated, where a (KD) x charge-relay peptide (designed in this study) led to the most reproducible and selective silica deposition. A homogenous coating of the biotemplate and tight control of shell thickness were achieved.
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Affiliation(s)
- Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Axel Seidenstücker
- Institute of Solid State Physics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Alexander Welle
- Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sabine Eiben
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Petia Atanasova
- Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Nina Stitz
- Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Alfred Plettl
- Institute of Solid State Physics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Joachim Bill
- Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Hartmut Gliemann
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Dirk Rothenstein
- Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Fania Geiger
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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21
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Baio JE, Zane A, Jaeger V, Roehrich AM, Lutz H, Pfaendtner J, Drobny GP, Weidner T. Diatom mimics: directing the formation of biosilica nanoparticles by controlled folding of lysine-leucine peptides. J Am Chem Soc 2014; 136:15134-7. [PMID: 25285787 DOI: 10.1021/ja5078238] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Silaffins, long chain polyamines, and other biomolecules found in diatoms are involved in the assembly of a large number of silica nanostructures under mild, ambient conditions. Nanofabrication researchers have sought to mimic the diatom's biosilica production capabilities by engineering proteins to resemble aspects of naturally occurring biomolecules. Such mimics can produce monodisperse biosilica nanospheres, but in vitro production of the variety of intricate biosilica nanostructures that compose the diatom frustule is not yet possible. In this study we demonstrate how LK peptides, composed solely of lysine (K) and leucine (L) amino acids arranged with varying hydrophobic periodicities, initiate the formation of different biosilica nanostructures in vitro. When L and K residues are arranged with a periodicity of 3.5 the α-helical form of the LK peptide produces monodisperse biosilica nanospheres. However, when the LK periodicity is changed to 3.0, corresponding to a 310 helix, the morphology of the nanoparticles changes to elongated rod-like structures. β-strand LK peptides with a periodicity of 2.0 induce wire-like silica morphologies. This study illustrates how the morphology of biosilica can be changed simply by varying the periodicity of polar and nonpolar amino acids.
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Affiliation(s)
- Joe E Baio
- School of Chemical, Biological, and Environmental Engineering, Oregon State University , Corvallis, Oregon 97331, United States
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