Effect of oxygen and nitrogen functionalization on the physical and electronic structure of graphene

Covalent functionalization of graphene offers opportunities for tailoring its properties and is an unavoidable consequence of some graphene synthesis techniques. However, the changes induced by the functionalization are not well understood. By using atomic sources to control the extent of the oxygen and nitrogen functionalization, we studied the evolution in the structure and properties at the atomic scale. Atomic oxygen reversibly introduces epoxide groups whilst, under similar conditions, atomic nitrogen irreversibly creates diverse functionalities including substitutional, pyridinic, and pyrrolic nitrogen. Atomic oxygen leaves the Fermi energy at the Dirac point (i.e., undoped), whilst atomic nitrogen results in a net n-doping; however, the experimental results are consistent with the dominant electronic effect for both being a transition from delocalized to localized states, and hence the loss of the signature electronic structure of graphene

Structural variation, dynamics, and catalytic application of palladium(II) complexes of di-N-heterocyclic carbene-amine ligands

A series of palladium(II) complexes incorporating di-NHC-amine ligands has been prepared and their structural, dynamic and catalytic behaviour investigated. The complexes [trans-(k(2)-(CN)-C-tBu(Bn)CN(Bn)C-tBu)PdCl2] (12) and [trans-(kappa(2)-(CN)-C-Mes(H)C-Mes)PdCl2] (13) do not exhibit interaction between the amine nitrogen and palladium atom respectively. NMR spectroscopy between - 40 and 25 degrees C shows that the di-NHC-amine ligand is flexible expressing C-s symmetry and for 13 rotation of the mesityl groups is prevented. In the related C-1 complex [(kappa(3)-(CN)-C-tBu(H)C-tBu)PdCl][CI] (14) coordination of NHC moieties and amine nitrogen atom is observed between -40 and 25 degrees C. Reaction between 12 - 14 and two equivalents of AgBF4 in acetonitrile gives the analogous complexes [trans-(kappa(2)-(CN)-C-tBu(Bn)C-tBu)PdCl2] (12) and [trans-(kappa(CN)-C-2Mes(H)C-Mes)PdCl2] (13) do not exhibit interaction between the amine nitrogen and palladium atom respectively. NMR spectroscopy between -40 ans 25 degrees C shows the di-NHC-amine ligand is flexible expressing C-s symmetry and for 13 rotation of the mesityl groups is prevented. In the related C-1 complex [kappa(3)-(CN)-C-tBu(H)C-tBu)PdCI][CI] (14) coordination of NHC moieties and amine nitrogen atom is observed between -40 and 25 degrees C.Reaction between 12-14 and two equivalents of AgBF4 in acetonitrile gives the analogous complexes [trans-(kappa(2)-(CN)-C-tBu(H)(CPd)-Pd-tBu(MeCN)(2)][BF4](2) (15), [trans-(kappa(CN)-C-2Mes(H)C-Mes)Pd(MeCN)(2)[BF4](2 (16)) and [(kappa(3)-(CN)-C-tBu(H)C-tBu)Pd(MeCN)][BF4](2) (17) indicating that ligand structure determines amine coordination. The single crystal X-ray structures of 12, 17 and two ligand imidazolium salt precursors C-tBu(H)N(Bn)C(H) (tBu)][CI](2) (2) and [C-tBu(H) N(H)C(H)(tBu)][BPh4](2) (4) have been determined. Complexes 12-14 and 15-17 have been shown to be active precatalysts for Heck and hydroamination reactions respectively

Entropy creation inside black holes points to observer complementarity

Heating processes inside large black holes can produce tremendous amounts of entropy. Locality requires that this entropy adds on space-like surfaces, but the resulting entropy (10^10 times the Bekenstein-Hawking entropy in an example presented in the companion paper) exceeds the maximum entropy that can be accommodated by the black hole's degrees of freedom. Observer complementarity, which proposes a proliferation of non-local identifications inside the black hole, allows the entropy to be accommodated as long as individual observers inside the black hole see less than the Bekenstein-Hawking entropy. In the specific model considered with huge entropy production, we show that individual observers do see less than the Bekenstein-Hawking entropy, offering strong support for observer complementarity.Comment: 13 pages. This is a companion paper to arXiv:0801.4415; Added reference

Hub Promiscuity in Protein-Protein Interaction Networks

Hubs are proteins with a large number of interactions in a protein-protein interaction network. They are the principal agents in the interaction network and affect its function and stability. Their specific recognition of many different protein partners is of great interest from the structural viewpoint. Over the last few years, the structural properties of hubs have been extensively studied. We review the currently known features that are particular to hubs, possibly affecting their binding ability. Specifically, we look at the levels of intrinsic disorder, surface charge and domain distribution in hubs, as compared to non-hubs, along with differences in their functional domains

Multi-scale sequence correlations increase proteome structural disorder and promiscuity

Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone to non-specific interactions, and structurally disordered. We predict that multi-scale correlations of amino acid positions within protein sequences statistically enhance the propensity for promiscuous intra- and inter-protein binding. We show that sequence correlations between amino acids of the same type are statistically enhanced in structurally disordered proteins and in hubs of organismal proteomes. We also show that structurally disordered proteins possess a significantly higher degree of sequence order than structurally ordered proteins. We develop an analytical theory for this effect and predict the robustness of our conclusions with respect to the amino acid composition and the form of the microscopic potential between the interacting sequences. Our findings have implications for understanding molecular mechanisms of protein aggregation diseases induced by the extension of sequence repeats

Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo

Intrinsically disordered/unstructured proteins (IDPs) are extremely sensitive to proteolysis in vitro, but show no enhanced degradation rates in vivo. Their existence and functioning may be explained if IDPs are preferentially associated with chaperones in the cell, which may offer protection against degradation by proteases. To test this inference, we took pairwise interaction data from high-throughput interaction studies and analyzed to see if predicted disorder correlates with the tendency of chaperone binding by proteins. Our major finding is that disorder predicted by the IUPred algorithm actually shows negative correlation with chaperone binding in E. coli, S. cerevisiae, and metazoa species. Since predicted disorder positively correlates with the tendency of partner binding in the interactome, the difference between the disorder of chaperone-binding and non-binding proteins is even more pronounced if normalized to their overall tendency to be involved in pairwise protein–protein interactions. We argue that chaperone binding is primarily required for folding of globular proteins, as reflected in an increased preference for chaperones of proteins in which at least one Pfam domain exists. In terms of the functional consequences of chaperone binding of mostly disordered proteins, we suggest that its primary reason is not the assistance of folding, but promotion of assembly with partners. In support of this conclusion, we show that IDPs that bind chaperones also tend to bind other proteins

Low-complexity regions within protein sequences have position-dependent roles

<p>Abstract</p> <p>Background</p> <p>Regions of protein sequences with biased amino acid composition (so-called Low-Complexity Regions (LCRs)) are abundant in the protein universe. A number of studies have revealed that i) these regions show significant divergence across protein families; ii) the genetic mechanisms from which they arise lends them remarkable degrees of compositional plasticity. They have therefore proved difficult to compare using conventional sequence analysis techniques, and functions remain to be elucidated for most of them. Here we undertake a systematic investigation of LCRs in order to explore their possible functional significance, placed in the particular context of Protein-Protein Interaction (PPI) networks and Gene Ontology (GO)-term analysis.</p> <p>Results</p> <p>In keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs. More specifically, our study suggests i) that LCRs are preferentially positioned towards the protein sequence extremities and, in contrast with centrally-located LCRs, such terminal LCRs show a correlation between their lengths and degrees of connectivity, and ii) that centrally-located LCRs are enriched with transcription-related GO terms, while terminal LCRs are enriched with translation and stress response-related terms.</p> <p>Conclusions</p> <p>Our results suggest not only that LCRs may be involved in flexible binding associated with specific functions, but also that their positions within a sequence may be important in determining both their binding properties and their biological roles.</p

A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks

Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery