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White S.J.,University of Leeds | Morton D.W.A.,University of Leeds | Cheah B.C.,University of Leeds | Bronowska A.,Heidelberg Institute for Theoretical Studies gGmbH | And 4 more authors.
Langmuir | Year: 2012

The coiled coil is a widespread protein motif responsible for directing the assembly of a wide range of protein complexes. To date, research has focused largely on the solution phase assembly of coiled-coil complexes. Here, we describe an investigation into coiled-coil heterodimer assembly where one of the peptides is immobilized directly onto a gold electrode. Immobilization is achieved by the introduction of a unique cysteine residue at the C terminus, allowing for covalent and orientated attachment to a thiol-reactive surface, here the gold electrode. We show an electrochemical impedance of the resulting self-assembled polypeptide monolayer around |Z| = 4 × 104 Ω cm2 at 100 mHz with a minimum phase angle of -84°, consistent with the formation of a densely packed, insulating layer. The thickness of the peptide monolayer, as measured using ellipsometry, is around 3 nm, close to that expected for a self-assembled monolayer assembled from helical peptides. Crucially, we find that the efficiency of dimerization between a peptide in solution and its coiled-coil partner peptide immobilized on a surface is strongly dependent upon the density of the immobilized peptide layer, with dimer assembly being strongly suppressed by high-density peptide monolayers. We thus develop an approach for controlling the density of the immobilized peptide by diluting the monolayer with a thiolated, random-coil peptide to modulate dimerization efficiency and demonstrate electrochemical detection of highly specific, coiled-coil heterodimer on-surface assembly. © 2012 American Chemical Society.

Cheng S.,Chinese Academy of Sciences | Cetinkaya M.,Chinese Academy of Sciences | Cetinkaya M.,University of Heidelberg | Grater F.,Chinese Academy of Sciences | And 2 more authors.
Biophysical Journal | Year: 2010

How nature tunes sequences of disordered protein to yield the desired coiling properties is not yet well understood. To shed light on the relationship between protein sequence and elasticity, we here investigate four different natural disordered proteins with elastomeric function, namely: FG repeats in the nucleoporins; resilin in the wing tendon of dragonfly; PPAK in the muscle protein titin; and spider silk. We obtain force-extension curves for these proteins from extensive explicit solvent molecular dynamics simulations, which we compare to purely entropic coiling by modeling the four proteins as entropic chains. Although proline and glycine content are in general indicators for the entropic elasticity as expected, divergence from simple additivity is observed. Namely, coiling propensities correlate with polyproline II content more strongly than with proline content, and given a preponderance of glycines for sufficient backbone flexibility, nonlocal interactions such as electrostatic forces can result in strongly enhanced coiling, which results for the case of resilin in a distinct hump in the force-extension curve. Our results, which are directly testable by force spectroscopy experiments, shed light on how evolution has designed unfolded elastomeric proteins for different functions. © 2010 by the Biophysical Society.

Ponzetto S.P.,University of Heidelberg | Strube M.,Heidelberg Institute for Theoretical Studies gGmbH
Artificial Intelligence | Year: 2011

The category system in Wikipedia can be taken as a conceptual network. We label the semantic relations between categories using methods based on connectivity in the network and lexico-syntactic matching. The result is a large scale taxonomy. For evaluation we propose a method which (1) manually determines the quality of our taxonomy, and (2) automatically compares its coverage with ResearchCyc, one of the largest manually created ontologies, and the lexical database WordNet. Additionally, we perform an extrinsic evaluation by computing semantic similarity between words in benchmarking datasets. The results show that the taxonomy compares favorably in quality and coverage with broad-coverage manually created resources. © 2011 Elsevier B.V. All rights reserved.

White S.J.,University of Leeds | Johnson S.D.,University of York | Sellick M.A.,University of Leeds | Bronowska A.,Heidelberg Institute for Theoretical Studies gGmbH | And 2 more authors.
Angewandte Chemie - International Edition | Year: 2015

Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface-phase studies, in which molecular densities generally far exceed those observed in solution. Using on-surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a structural transition between a-helical and random coil conformation upon changes in pH and ionic concentration, but critically the threshold for conformational change is altered dramatically by molecular crowding within the peptide monolayer. This study highlights the often overlooked role molecular crowding plays in regulating molecular structure and function in surface-phase studies of biological molecules. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.

Dudek M.,University of Warsaw | Dudek M.,Polish Academy of Sciences | Dudek M.,Medical University of Warsaw | Romanowska J.,University of Warsaw | And 4 more authors.
Biochimie | Year: 2014

Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding. © 2014 The Authors. Published by Elsevier Masson SAS.

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