Publications by authors named "Alberto Gomez-Casado"

11 Publications

  • Page 1 of 1

Supramolecularly oriented immobilization of proteins using cucurbit[8]uril.

Langmuir 2012 Nov 12;28(47):16364-71. Epub 2012 Nov 12.

Molecular Nanofabrication Group, Department of Science and Technology, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.

A supramolecular strategy is used for oriented positioning of proteins on surfaces. A viologen-based guest molecule is attached to the surface, while a naphthol guest moiety is chemoselectively ligated to a yellow fluorescent protein. Cucurbit[8]uril (CB[8]) is used to link the proteins onto surfaces through specific charge-transfer interactions between naphthol and viologen inside the CB cavity. The assembly process is characterized using fluorescence and atomic force microscopy, surface plasmon resonance, IR-reflective absorption, and X-ray photoelectron spectroscopy measurements. Two different immobilization routes are followed to form patterns of the protein ternary complexes on the surfaces. Each immobilization route consists of three steps: (i) attaching the viologen to the glass using microcontact chemistry, (ii) blocking, and (iii) either incubation or microcontact printing of CB[8] and naphthol guests. In both cases uniform and stable fluorescent patterns are fabricated with a high signal-to-noise ratio. Control experiments confirm that CB[8] serves as a selective linking unit to form stable and homogeneous ternary surface-bound complexes as envisioned. The attachment of the yellow fluorescent protein complexes is shown to be reversible and reusable for assembly as studied using fluorescence microscopy.
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http://dx.doi.org/10.1021/la303987cDOI Listing
November 2012

Reversible and oriented immobilization of ferrocene-modified proteins.

J Am Chem Soc 2012 Nov 8;134(46):19199-206. Epub 2012 Nov 8.

Molecular Nanofabrication Group, Department of Science and Technology, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.

Adopting supramolecular chemistry for immobilization of proteins is an attractive strategy that entails reversibility and responsiveness to stimuli. The reversible and oriented immobilization and micropatterning of ferrocene-tagged yellow fluorescent proteins (Fc-YFPs) onto β-cyclodextrin (βCD) molecular printboards was characterized using surface plasmon resonance (SPR) spectroscopy and fluorescence microscopy in combination with electrochemistry. The proteins were assembled on the surface through the specific supramolecular host-guest interaction between βCD and ferrocene. Application of a dynamic covalent disulfide lock between two YFP proteins resulted in a switch from monovalent to divalent ferrocene interactions with the βCD surface, yielding a more stable protein immobilization. The SPR titration data for the protein immobilization were fitted to a 1:1 Langmuir-type model, yielding K(LM) = 2.5 × 10(5) M(-1) and K(i,s) = 1.2 × 10(3) M(-1), which compares favorably to the intrinsic binding constant presented in the literature for the monovalent interaction of ferrocene with βCD self-assembled monolayers. In addition, the SPR binding experiments were qualitatively simulated, confirming the binding of Fc-YFP in both divalent and monovalent fashion to the βCD monolayers. The Fc-YFPs could be patterned on βCD surfaces in uniform monolayers, as revealed using fluorescence microscopy and atomic force microscopy measurements. Both fluorescence microscopy imaging and SPR measurements were carried out with the in situ capability to perform cyclic voltammetry and chronoamperometry. These studies emphasize the repetitive desorption and adsorption of the ferrocene-tagged proteins from the βCD surface upon electrochemical oxidation and reduction, respectively.
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http://dx.doi.org/10.1021/ja308450nDOI Listing
November 2012

Interlaboratory round robin on cantilever calibration for AFM force spectroscopy.

Ultramicroscopy 2011 Dec 24;111(12):1659-69. Epub 2011 Sep 24.

Scanning Probe Microscopy, Radboud University Nijmegen, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands.

Single-molecule force spectroscopy studies performed by Atomic Force Microscopes (AFMs) strongly rely on accurately determined cantilever spring constants. Hence, to calibrate cantilevers, a reliable calibration protocol is essential. Although the thermal noise method and the direct Sader method are frequently used for cantilever calibration, there is no consensus on the optimal calibration of soft and V-shaped cantilevers, especially those used in force spectroscopy. Therefore, in this study we aimed at establishing a commonly accepted approach to accurately calibrate compliant and V-shaped cantilevers. In a round robin experiment involving eight different laboratories we compared the thermal noise and the Sader method on ten commercial and custom-built AFMs. We found that spring constants of both rectangular and V-shaped cantilevers can accurately be determined with both methods, although the Sader method proved to be superior. Furthermore, we observed that simultaneous application of both methods on an AFM proved an accurate consistency check of the instrument and thus provides optimal and highly reproducible calibration. To illustrate the importance of optimal calibration, we show that for biological force spectroscopy studies, an erroneously calibrated cantilever can significantly affect the derived (bio)physical parameters. Taken together, our findings demonstrated that with the pre-established protocol described reliable spring constants can be obtained for different types of cantilevers.
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http://dx.doi.org/10.1016/j.ultramic.2011.09.012DOI Listing
December 2011

Recognition properties of cucurbit[7]uril self-assembled monolayers studied with force spectroscopy.

Langmuir 2011 Sep 22;27(18):11508-13. Epub 2011 Aug 22.

Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500AE, Enschede, The Netherlands.

Specific (host-guest) and unspecific (substrate-guest) interactions between self-assembled monolayers of cucurbit[7]uril (CB[7]) on gold (Au) substrates and neutral adamantyl (Ad) guests were resolved by studying these interactions at the single molecule level using dynamic force spectroscopy. The dissociation rate constants of the Ad-Au and the Ad-CB[7] interactions were 0.3 s(-1) and 0.03 s(-1), respectively, indicating that the specific binding is more stable. The probability of observing a specific interaction (40 ± 9%) is similar to the reported surface coverages of CB[7] monolayers on Au substrates. The higher strength and stability of the Ad-CB[7] interactions explains why, although presenting an imperfect coverage, CB[n] monolayers can be used successfully as a platform for surface immobilization.
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http://dx.doi.org/10.1021/la202346rDOI Listing
September 2011

Probing multivalent interactions in a synthetic host-guest complex by dynamic force spectroscopy.

J Am Chem Soc 2011 Jul 24;133(28):10849-57. Epub 2011 Jun 24.

Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede, The Netherlands.

Multivalency is present in many biological and synthetic systems. Successful application of multivalency depends on a correct understanding of the thermodynamics and kinetics of this phenomenon. In this Article, we address the stability and strength of multivalent bonds with force spectroscopy techniques employing a synthetic adamantane/β-cyclodextrin model system. Comparing the experimental findings to theoretical predictions for the rupture force and the kinetic off-rate, we find that when the valency of the complex is increased from mono- to di- to trivalent, there is a transition from quasi-equilibrium, with a constant rupture force of 99 pN, to a kinetically dependent state, with loading-rate-dependent rupture forces from 140 to 184 pN (divalent) and 175 to 210 pN (trivalent). Additional binding geometries, parallel monovalent ruptures, single-bound divalent ruptures, and single- and double-bound trivalent ruptures are identified. The experimental kinetic off-rates of the multivalent complexes show that the stability of the complexes is significantly enhanced with the number of bonds, in agreement with the predictions of a noncooperative multivalent model.
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http://dx.doi.org/10.1021/ja2016125DOI Listing
July 2011

Gradient-driven motion of multivalent ligand molecules along a surface functionalized with multiple receptors.

Nat Chem 2011 Apr 6;3(4):317-22. Epub 2011 Mar 6.

Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands.

The kinetics of multivalent (multisite) interactions at interfaces is poorly understood, despite its fundamental importance for molecular or biomolecular motion and molecular recognition events at biological interfaces. Here, we use fluorescence microscopy to monitor the spreading of mono-, di- and trivalent ligand molecules on a receptor-functionalized surface, and perform multiscale computer simulations to understand the surface diffusion mechanisms. Analogous to chemotaxis, we found that the spreading is directional (along a developing gradient of vacant receptor sites) and is strongly dependent on ligand valency and concentration of a competing monovalent receptor in solution. We identify multiple surface diffusion mechanisms, which we call walking, hopping and flying. The study shows that the interfacial behaviour of multivalent systems is much more complex than that of monovalent ones.
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http://dx.doi.org/10.1038/nchem.1005DOI Listing
April 2011

Direct patterning of covalent organic monolayers on silicon using nanoimprint lithography.

Langmuir 2010 Sep;26(17):14210-5

Molecular Nanofabrication group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.

Two fabrication schemes are reported for the direct patterning of organic monolayers on oxide-free silicon, combining top-down nanoimprint lithography and bottom-up monolayer formation. The first approach was designed to form monolayer patterns on the imprinted areas, while the second approach was designed for monolayer formation outside of the imprinted features. By both approaches, covalently bonded Si-C monolayer patterns with feature sizes ranging from 100 nm to 100 microm were created via a hydrosilylation procedure using diluted reagents. Both unfunctionalized and omega-functionalized alkenes were patterned successfully.
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http://dx.doi.org/10.1021/la101445nDOI Listing
September 2010

Ordered and oriented supramolecular n/p-heterojunction surface architectures: completion of the primary color collection.

J Am Chem Soc 2009 Aug;131(31):11106-16

Department of Organic, University of Geneva, Geneva, Switzerland.

In this study, we describe synthesis, characterization, and zipper assembly of yellow p-oligophenyl naphthalenediimide (POP-NDI) donor-acceptor hybrids. Moreover, we disclose, for the first time, results from the functional comparison of zipper and layer-by-layer (LBL) assembly as well as quartz crystal microbalance (QCM), atomic force microscopy (AFM), and molecular modeling data on zipper assembly. Compared to the previously reported blue and red NDIs, yellow NDIs are more pi-acidic, easier to reduce, and harder to oxidize. The optoelectronic matching achieved in yellow POP-NDIs is reflected in quantitative and long-lived photoinduced charge separation, comparable to their red and much better than their blue counterparts. The direct comparison of zipper and LBL assemblies reveals that yellow zippers generate more photocurrent than blue zippers as well as LBL photosystems. Continuing linear growth found in QCM measurements demonstrates that photocurrent saturation at the critical assembly thickness occurs because more charges start to recombine before reaching the electrodes and not because of discontinued assembly. The found characteristics, such as significant critical thickness, strong photocurrents, large fill factors, and, according to AFM images, smooth surfaces, are important for optoelectronic performance and support the existence of highly ordered architectures.
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http://dx.doi.org/10.1021/ja9030648DOI Listing
August 2009

Porous multilayer-coated PDMS stamps for protein printing.

Langmuir 2009 Dec;25(24):13972-7

Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede, The Netherlands.

A polyelectrolyte multilayer was assembled on top of a patterned PDMS stamp employing the layer-by-layer (LbL) assembly technique. By post-treatment with a base and further cross-linking, a porous multilayer-coated PDMS composite stamp was obtained. With the pore structures acting as an ink reservoir, the multiple printing of proteins was successfully achieved without the need to re-ink the stamp.
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http://dx.doi.org/10.1021/la901797nDOI Listing
December 2009

Hooke: an open software platform for force spectroscopy.

Bioinformatics 2009 Jun 31;25(11):1428-30. Epub 2009 Mar 31.

Department of Biochemistry, University of Bologna, Bologna, Italy.

Summary: Hooke is an open source, extensible software intended for analysis of atomic force microscope (AFM)-based single molecule force spectroscopy (SMFS) data. We propose it as a platform on which published and new algorithms for SMFS analysis can be integrated in a standard, open fashion, as a general solution to the current lack of a standard software for SMFS data analysis. Specific features and support for file formats are coded as independent plugins. Any user can code new plugins, extending the software capabilities. Basic automated dataset filtering and semi-automatic analysis facilities are included.

Availability: Software and documentation are available at (http://code.google.com/p/hooke). Hooke is a free software under the GNU Lesser General Public License.
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http://dx.doi.org/10.1093/bioinformatics/btp180DOI Listing
June 2009
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