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From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica

Published on Jan 1, 2019in Physical Chemistry Chemical Physics 3.57
· DOI :10.1039/c8cp07011c
Daniel Oliver1
Estimated H-index: 1
(NTU: Nottingham Trent University),
Monika Michaelis2
Estimated H-index: 2
(NTU: Nottingham Trent University)
+ 2 AuthorsCarole C. Perry44
Estimated H-index: 44
(NTU: Nottingham Trent University)
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Abstract
Polypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications. Following the identification of a strong silica binder (LDHSLHS) by phage display, we conduct structural analysis of the polypeptide at the interface with amorphous silica nanoparticles in an aqueous environment. Our approach relies on modelling infrared and Raman spectral responses using predictions of molecular dynamics simulations and quantum studies of the normal modes for several potential structures. By simultaneously fitting both infrared and Raman responses in the amide spectral region, we show that the main structural conformer has a beta-like central region and helix-twisted terminals. Classical simulations, as conducted previously (Chem. Mater., 2014, 26, 5725), predict that the association of the main structure with the interface is stimulated by electrostatic interactions though surface binding also requires spatially distributed sodium ions to compensate for negatively charged acidic silanol groups. Accordingly, diffusion of sodium ions would contribute to a stochastic character of the peptide association with the surface. Consistent with the described dynamics at the interface, the results obtained from isothermal titration calorimetry (ITC) confirm a significant enhancement of polypeptide binding to silica at higher concentrations of Na+. The results of this study suggest that the tertiary structure of a phage capsid protein plays a significant role in regulating the conformation of peptide LDHSLHS, increasing its binding to silica during the phage display process. The results presented here support design-led engineering of polypeptide–silica nanocomposites for bio-technological applications.
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Published on Jun 7, 2018in Journal of Physical Chemistry A 2.64
Victor Volkov8
Estimated H-index: 8
(NTU: Nottingham Trent University),
David J. Belton14
Estimated H-index: 14
(NTU: Nottingham Trent University),
Carole C. Perry44
Estimated H-index: 44
(NTU: Nottingham Trent University)
Structural properties of bioinorganic composites are of current interest in the areas of drug delivery, bone repair, and biomimetics. In such composite systems, structural analysis is enhanced when we combine methods of spectroscopy and simulation. Depending on size and shape, structural discontinuities of inorganic matter may modulate the optical response of a bound molecule. Using density functional theory, we explore the effects of a local field next to the surface of a silica cluster on freq...
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Anja Muždalo1
Estimated H-index: 1
(MPG: Max Planck Society),
Peter Saalfrank1
Estimated H-index: 1
+ 1 AuthorsMark Santer7
Estimated H-index: 7
(MPG: Max Planck Society)
Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomer...
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Phillip Barden6
Estimated H-index: 6
(NJIT: New Jersey Institute of Technology),
Hollister W. Herhold1
Estimated H-index: 1
(AMNH: American Museum of Natural History),
David A. Grimaldi40
Estimated H-index: 40
(AMNH: American Museum of Natural History)
An unusual Cretaceous trap jaw ant is described from Burmese amber dated to the Late Cretaceous. Linguamyrmex vladi gen.n. sp.n. is distinguished by an unusual suite of morphological characters indicating specialized predatory behaviour and an adaptive strategy no longer found among modern ant lineages. The clypeus, highly modified as in other closely related haidomyrmecine hell ants, is equipped with a paddle-like projection similar to Ceratomyrmex. X-ray imaging reveals that this clypeal paddl...
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Jaison Arivalagan4
Estimated H-index: 4
(University of Paris),
Tejaswi Yarra3
Estimated H-index: 3
(Edin.: University of Edinburgh)
+ 5 AuthorsSophie Berland3
Estimated H-index: 3
(University of Paris)
Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical properties of the shell itself. Although, there is a general consensus that a minimum basic protein tool kit is required for shell construction, to date, this remains undefined. In thi...
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Alexandre G. de Brevern22
Estimated H-index: 22
The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that c...
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Maroua Saadaoui3
Estimated H-index: 3
(Tunis University),
Iñigo Fernández5
Estimated H-index: 5
(Complutense University of Madrid)
+ 5 AuthorsReynaldo Villalonga31
Estimated H-index: 31
(Complutense University of Madrid)
Abstract A novel electroanalytical strategy for copper and ascorbic acid detection was developed by using a nanostructured electrode surface mechanized with a DNAzyme-based molecular gate. This sensing interface was constructed by first electrodeposition of a mesoporous silica thin film on Au electrodes and further assembly of a Cu(II)-specific DNAzyme. The biosensing assay was based on the Cu(II) and ascorbic acid responsible activation of the DNAzyme, which acted as a molecular switch able to ...
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Published on Oct 14, 2014in Chemistry of Materials 10.16
Fateme S. Emami6
Estimated H-index: 6
,
Valeria Puddu5
Estimated H-index: 5
+ 4 AuthorsHendrik Heinz34
Estimated H-index: 34
Silica nanostructures are biologically available and find wide applications for drug delivery, catalysts, separation processes, and composites. However, specific adsorption of biomolecules on silica surfaces and control in biomimetic synthesis remain largely unpredictable. In this contribution, the variability and control of peptide adsorption on silica nanoparticle surfaces are explained as a function of pH, particle diameter, and peptide electrostatic charge using molecular dynamics simulation...
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Joanna Borek3
Estimated H-index: 3
(UZH: University of Zurich),
Fivos Perakis9
Estimated H-index: 9
(UZH: University of Zurich),
Peter Hamm18
Estimated H-index: 18
(UZH: University of Zurich)
Using 3D infrared (IR) exchange spectroscopy, the ultrafast hydrogen-bond forming and breaking (i.e., complexation) kinetics of phenol to benzene in a benzene/CCl 4 mixture is investigated. By introducing a third time point at which the hydrogen-bonding state of phenol is measured (in comparison with 2D IR exchange spectroscopy), the spectroscopic method can serve as a critical test of whether the spectroscopic coordinate used to observe the exchange process is a memory-free, or Markovian, coord...
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Published on Jun 26, 2014in Journal of Physical Chemistry B 2.92
Fan Jiang14
Estimated H-index: 14
,
Chen-Yang Zhou3
Estimated H-index: 3
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Yun-Dong Wu46
Estimated H-index: 46
Traditional protein force fields use one set of parameters for most of the 20 amino acids (AAs), allowing transferability of the parameters. However, a significant shortcoming is the difficulty to fit the Ramachandran plots of all AA residues simultaneously, affecting the accuracy of the force field. In this Feature Article, we report a new strategy for protein force field parametrization. Backbone and side-chain conformational distributions of all 20 AA residues obtained from protein coil libra...
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Published on Apr 22, 2014in Chemistry of Materials 10.16
Fateme S. Emami6
Estimated H-index: 6
,
Valeria Puddu5
Estimated H-index: 5
+ 4 AuthorsHendrik Heinz34
Estimated H-index: 34
Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last 30 years and reduces uncertainties in computed interfacial properties relative to experiment from several 100% to less than 5%. In addit...
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