Mulder F.A.A.,University of Groningen |
Filatov M.,Zernike Institute for Advanced Materials
Chemical Society Reviews | Year: 2010
In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the accuracy of different computational methods are discussed. It is anticipated that incorporating theoretical information on chemical shifts will increase the accuracy of protein structures, in the solid and liquid state alike, and extend the applicability of NMR spectroscopy to ever larger systems. © 2010 The Royal Society of Chemistry.
Greer J.R.,California Institute of Technology |
De Hosson J.T.M.,Zernike Institute for Advanced Materials
Progress in Materials Science | Year: 2011
A material strength depends on its microstructure, which in turn, is controlled by an engineering process. Strengthening mechanisms like work hardening, precipitate, and grain boundary strengthening can alter the strength of a material in a predictive, quantitative manner and are readily linked to the deformation mechanism. This quantification strongly depends on the characteristic length scale of a particular microstructure, thereby dictating bulk material's strength as a function of, for example, grain or precipitate size, twin boundary spacing, or dislocation density. This microstructural, or intrinsic, size governs the mechanical properties and post-elastic material deformation at all sample dimensions, as the classical definition of "ultimate tensile strength" deems it to be "an intensive property, therefore its value does not depend on the size of the test specimen." Yet in the last 5 years, the vast majority of uniaxial deformation experiments and computations on small-scale metallic structures unambiguously demonstrated that at the micron and sub-micron scales, this definition no longer holds true. In fact, it has been shown that in single crystals the ultimate tensile strength and the yield strength scale with external sample size in a power law fashion, sometimes attaining a significant fraction of material's theoretical strength, and exhibiting the now-commonly-known phenomenon "smaller is stronger." Understanding of this "extrinsic size effect" at small scales is not yet mature and is currently a topic of rigorous investigations. As both the intrinsic (i.e. microstructural) and extrinsic (i.e. sample size) dimensions play a non-trivial role in the mechanical properties and material deformation mechanisms, it is critical to develop an understanding of their interplay and mutual effects on the mechanical properties and material deformation, especially in small-scale structures. This review focuses on providing an overview of metal-based material classes whose properties as a function of external size have been investigated and provides a critical discussion on the combined effects of intrinsic and extrinsic sizes on the material deformation behavior. © 2011 Elsevier Ltd. All rights reserved.
Stratmann S.A.,Zernike Institute for Advanced Materials |
Van Oijen A.M.,Zernike Institute for Advanced Materials
Chemical Society Reviews | Year: 2014
A cell can be thought of as a highly sophisticated micro factory: in a pool of billions of molecules-metabolites, structural proteins, enzymes, oligonucleotides-multi-subunit complexes assemble to perform a large number of basic cellular tasks, such as DNA replication, RNA/protein synthesis or intracellular transport. By purifying single components and using them to reconstitute molecular processes in a test tube, researchers have gathered crucial knowledge about mechanistic, dynamic and structural properties of biochemical pathways. However, to sort this information into an accurate cellular road map, we need to understand reactions in their relevant context within the cellular hierarchy, which is at the individual molecule level within a crowded, cellular environment. Reactions occur in a stochastic fashion, have short-lived and not necessarily well-defined intermediates, and dynamically form functional entities. With the use of single-molecule techniques these steps can be followed and detailed kinetic information that otherwise would be hidden in ensemble averaging can be obtained. One of the first complex cellular tasks that have been studied at the single-molecule level is the replication of DNA. The replisome, the multi-protein machinery responsible for copying DNA, is built from a large number of proteins that function together in an intricate and efficient fashion allowing the complex to tolerate DNA damage, roadblocks or fluctuations in subunit concentration. In this review, we summarize advances in single-molecule studies, both in vitro and in vivo, that have contributed to our current knowledge of the mechanistic principles underlying DNA replication. © 2014 The Royal Society of Chemistry.
Schnitzler T.,Zernike Institute for Advanced Materials |
Herrmann A.,Zernike Institute for Advanced Materials
Accounts of Chemical Research | Year: 2012
We live in a world full of synthetic materials, and the development of new technologies builds on the design and synthesis of new chemical structures, such as polymers. Synthetic macromolecules have changed the world and currently play a major role in all aspects of daily life. Due to their tailorable properties, these materials have fueled the invention of new techniques and goods, from the yogurt cup to the car seat belts. To fulfill the requirements of modern life, polymers and their composites have become increasingly complex. One strategy for altering polymer properties is to combine different polymer segments within one polymer, known as block copolymers. The microphase separation of the individual polymer components and the resulting formation of well defined nanosized domains provide a broad range of new materials with various properties. Block copolymers facilitated the development of innovative concepts in the fields of drug delivery, nanomedicine, organic electronics, and nanoscience.Block copolymers consist exclusively of organic polymers, but researchers are increasingly interested in materials that combine synthetic materials and biomacromolecules. Although many researchers have explored the combination of proteins with organic polymers, far fewer investigations have explored nucleic acid/polymer hybrids, known as DNA block copolymers (DBCs). DNA as a polymer block provides several advantages over other biopolymers. The availability of automated synthesis offers DNA segments with nucleotide precision, which facilitates the fabrication of hybrid materials with monodisperse biopolymer blocks. The directed functionalization of modified single-stranded DNA by Watson-Crick base-pairing is another key feature of DNA block copolymers. Furthermore, the appropriate selection of DNA sequence and organic polymer gives control over the material properties and their self-assembly into supramolecular structures. The introduction of a hydrophobic polymer into DBCs in aqueous solution leads to amphiphilic micellar structures with a hydrophobic polymer core and a DNA corona.In this Account, we discuss selected examples of recent developments in the synthesis, structure manipulation and applications of DBCs. We present achievements in synthesis of DBCs and their amplification based on molecular biology techniques. We also focus on concepts involving supramolecular assemblies and the change of morphological properties by mild stimuli. Finally, we discuss future applications of DBCs. DBC micelles have served as drug-delivery vehicles, as scaffolds for chemical reactions, and as templates for the self-assembly of virus capsids. In nanoelectronics, DNA polymer hybrids can facilitate size selection and directed deposition of single-walled carbon nanotubes in field effect transistor (FET) devices. © 2012 American Chemical Society.
Wilts B.D.,Zernike Institute for Advanced Materials
Proceedings. Biological sciences / The Royal Society | Year: 2012
The neotropical diamond weevil, Entimus imperialis, is marked by rows of brilliant spots on the overall black elytra. The spots are concave pits with intricate patterns of structural-coloured scales, consisting of large domains of three-dimensional photonic crystals that have a diamond-type structure. Reflectance spectra measured from individual scale domains perfectly match model spectra, calculated with anatomical data and finite-difference time-domain methods. The reflections of single domains are extremely directional (observed with a point source less than 5°), but the special arrangement of the scales in the concave pits significantly broadens the angular distribution of the reflections. The resulting virtually angle-independent green coloration of the weevil closely approximates the colour of a foliaceous background. While the close-distance colourful shininess of E. imperialis may facilitate intersexual recognition, the diffuse green reflectance of the elytra when seen at long-distance provides cryptic camouflage.
Marrink S.J.,Zernike Institute for Advanced Materials |
Tieleman D.P.,University of Calgary
Chemical Society Reviews | Year: 2013
The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model. © 2013 The Royal Society of Chemistry.
van Oijen A.M.,Zernike Institute for Advanced Materials
Current Opinion in Biotechnology | Year: 2011
Single-molecule fluorescence techniques have emerged as powerful tools to study biological processes at the molecular level. This review describes the application of these methods to the characterization of the kinetics of interaction between biomolecules. A large number of single-molecule assays have been developed that visualize association and dissociation kinetics in vitro by fluorescently labeling binding partners and observing their interactions over time. Even though recent progress has been significant, there are certain limitations to this approach. To allow the observation of individual, fluorescently labeled molecules requires low, nanomolar concentrations. I will discuss how such concentration requirements in single-molecule experiments limit their applicability to investigate intermolecular interactions and how recent technical advances deal with this issue. © 2010 Elsevier Ltd.
Baaden M.,University Paris Diderot |
Marrink S.J.,Zernike Institute for Advanced Materials
Current Opinion in Structural Biology | Year: 2013
Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are separately described, but we note the parallel development that is present in both research fields with three important themes: firstly, combining CG modelling with knowledge-based approaches to predict and refine protein-protein complexes; secondly, using physics-based CG models for de novo prediction of protein-protein complexes; and thirdly modelling of large scale protein aggregates. © 2013 Elsevier Ltd.
Kwak M.,Zernike Institute for Advanced Materials |
Herrmann A.,Zernike Institute for Advanced Materials
Chemical Society Reviews | Year: 2011
This review provides an overview of a relatively new class of bio-conjugates, DNA amphiphiles, which consist of oligonucleotides covalently bonded to synthetic hydrophobic units. The reader will find the basic principles for the structural design and preparation methods of the materials. Moreover, the self-assembly into superstructures of higher order will be highlighted. Finally, some potential applications will be described. © The Royal Society of Chemistry 2011.
Mostovoy M.,Zernike Institute for Advanced Materials
Nature Materials | Year: 2010
A team of researchers conducted a study to demonstrate that multiferroic materials with their coexisting ordered states of electric and magnetic dipoles created significant opportunities and found many technological applications. These materials were expected to find increasing use in many technological applications, such as magnetoelectric random-access memory. One of the key ways to achieve this goal was demonstrated in the form of of significant control of electric polarization by an applied magnetic field in a number of compounds in which the electric dipoles were induced by ordered electron spins. Another potential route towards magnetoelectric switching relied on the specific properties of defects in multiferroic orders.