-
[show abstract]
[hide abstract]
ABSTRACT: Graphene is a 2D giant polycyclic aromatic molecule that provides opportunities for studying chemical reactions in two dimensions. H. Peng, Z. Liu, and co-workers have systematically investigated the influence of specific features of 2D molecules, such as their thickness, stacking order, single- and double-side upon graphene's radical reactivity by utilizing a free radical photochlorination as a probe. The result, described on page 1388, can contribute to a deeper understanding of dimensionality effects for the chemistry of 2D graphene.
Small 04/2013; 9(8):1387. · 8.35 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Graphene has stimulated enormous interest due to its intriguing structure and fascinating properties. The extremely high carrier mobility, mechanical flexibility, and optical transparency as well as the versatility for band structure engineering make graphene a promising candidate for next-generation carbon-based electronic devices. Graphene chemistry, the covalent functionalization of graphene as a 2D giant molecule, offers a promising direction to controllably tailor its properties through the introduction of various chemical decorations. One of the great challenges for graphene functionalization originates from its strong chemical stability, thus highly reactive chemical species are needed as the reactants. In recent years, novel photochemical approaches have been developed to achieve efficient graphene modification and bandgap modulation, following a general concept of "Photochemical Bandgap Engineering of Graphene". In this article, such kinds of photochemical graphene engineering are demonstrated, together with a brief discussion on the future directions, challenges, and opportunities in this fascinating research area.
Small 03/2013; · 8.35 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The carrier transport in boron nitride-embedded graphene (BNG) is studied using density functional theory coupled with the Boltzmann transport equation. Under a phonon scattering mechanism, the intrinsic carrier mobility of BNG at room temperature is tunable from 1.7 × 10(3) to 1.1 × 10(5) cm(2) V(-1) s(-1) when the bandgap is between 0.38 and 1.39 eV. Some specific BNG materials even show ultrahigh mobility up to 6.6 × 10(6) cm(2) V(-1) s(-1) , and the transport polarity (whether it is electron or hole transport) can be tailored by the application of a uniaxial strain. The wide mobility variation of BNG is attributed to the dependence of the effective mass and the deformation potential constant on the carbon concentration and width. The results indicate that BNG can have both a large on-off ratio and high carrier mobility and is thus a promising material for electronic devices.
Small 03/2013; · 8.35 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Graphene, a two-dimensional giant-molecule of sp(2) -bonded carbon atoms, provides a perfect platform for studying free radical reaction chemistry in two-dimensions, which holds promise to control the chemical functionality of graphene. Free-radical photochlorination of graphene is used as an example to investigate the thickness, stacking order, and single- and double-side dependent reactivity in graphene. Anomalously low reactivity is observed in the photochlorination of AB-stacked bilayer graphene in comparison with that of few-layer graphene. Double-sided chlorination of graphene shows higher reactivity and chlorine coverage than single-sided reaction. It is also experimentally and theoretically demonstrated that chlorine free radicals at low coverage prefer to form a stable charge-transfer complex with graphene, which highly enhances graphene's conductivity and simultaneously generates a pseudo-bandgap through noninvasive doping. Moreover, the initial accumulation of chlorine radicals is considered as the rate-determining step of photochlorination of graphene.
Small 03/2013; · 8.35 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: A frequently stated advantage of gapless graphene is its high carrier mobility. However, when a nonzero bandgap is opened, the mobility drops dramatically. The hardness to achieve high mobility and large on∕off ratio simultaneously limits the development of graphene electronics. To explore the underlying mechanism, we investigated the intrinsic mobility of armchair graphene nanoribbons (AGNRs) under phonon scattering by combining first-principles calculations and a tight-binding analysis. A linear dependence of the effective mass on bandgap was demonstrated to be responsible for the inverse mobility-gap relationship. The deformation-potential constant was found to be determined by the strain dependence of the Fermi energy and the bandgap, resulting in two mobility branches, and is essential for the high mobility of AGNRs. In addition, we showed that the transport polarity of AGNRs can be switched by applying a uniaxial strain.
The Journal of chemical physics 02/2013; 138(8):084701. · 3.09 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Specific protein-protein interactions are critical to cellular function. Structural flexibility and disorder-to-order transitions upon binding enable intrinsically disordered proteins (IDPs) to overcome steric restrictions and form complementary binding interfaces, and thus, IDPs are widely considered to have high specificity and low affinity for molecular recognition. However, flexibility may also enable IDPs to form complementary binding interfaces with misbinding partners, resulting in a great number of nonspecific interactions. Consequently, it is questionable whether IDPs really possess high specificity. In this work, we investigated this question from a thermodynamic viewpoint. We collected mutant thermodynamic data for 35 ordered protein complexes and 43 disordered protein complexes. We found that the enthalpy-entropy compensation for disordered protein complexes was more complete than that for ordered protein complexes. We further simulated the binding processes of ordered and disordered protein complexes under mutations. Simulation data confirmed the observation of experimental data analyses and further revealed that disordered protein complexes possessed smaller changes in binding free energy than ordered protein complexes under the same mutation perturbations. Therefore, interactions of IDPs are more malleable than those of ordered proteins due to their structural flexibility in the complex. Our results provide new clues for exploring the relationship between protein flexibility, adaptability, and specificity.
Chemistry 02/2013; · 5.93 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The full or partial unfolding of proteins is widely believed to play an essential role in three-dimensional domain swapping. However, there is little research that has rigorously evaluated the association between domain swapping and protein folding/unfolding. Here, we examined a kinetic model in which domain swapping occurred via the denatured state produced by the complete unfolding of proteins. The relationships between swapping kinetics and folding/unfolding thermodynamics were established, which were further adopted as criteria to show that the proposed mechanism dominates in three representative proteins: Cyanovirin-N (CV-N), the C-terminal domain of SARS-CoV main protease (M(pro) -C) and a single mutant of oxidized thioredoxin (Trx_W28A(ox) ).
Protein Science 12/2012; · 2.80 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Various graphene quantum dots (GQDs) embedded in a hexagonal BN sheet were studied theoretically using the tight binding model. The effective mass was analyzed as a function of the distance between neighboring GQDs. It was found that the effective mass increases exponentially as the distance increases, indicating that the confined states of GQDs are well conserved in these hybrid systems. Further studies revealed that a ubiquitous gap of 0.3-3 eV exists, the size of which is mainly governed by the GQD's dimensions whereas it is insensitive to edge structures. These results show that GQDs in BN are promising candidates for optoelectronics.
Physical Chemistry Chemical Physics 11/2012; · 3.57 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The unique ability of intrinsically disordered proteins (IDPs) to fold upon binding to partner molecules makes them functionally well-suited for cellular communication networks. For example, the folding-binding of different IDP sequences onto the same surface of an ordered protein provides a mechanism for signaling in a many-to-one manner. Here, we study the molecular details of this signaling mechanism by applying both Molecular Dynamics and Monte Carlo methods to S100B, a calcium-modulated homodimeric protein, and two of its IDP targets, p53 and TRTK-12. Despite adopting somewhat different conformations in complex with S100B and showing no apparent sequence similarity, the two IDP targets associate in virtually the same manner. As free chains, both target sequences remain flexible and sample their respective bound, natively [Formula: see text]-helical states to a small extent. Association occurs through an intermediate state in the periphery of the S100B binding pocket, stabilized by nonnative interactions which are either hydrophobic or electrostatic in nature. Our results highlight the importance of overall physical properties of IDP segments, such as net charge or presence of strongly hydrophobic amino acids, for molecular recognition via coupled folding-binding.
PLoS Computational Biology 09/2012; 8(9):e1002682. · 5.22 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: A tight-binding analytic framework is combined with first-principles calculations to reveal the mechanism underlying the strain
effects on electronic structures of graphene and graphene nanoribbons (GNRs). It provides a unified and precise formulation
of the strain effects under various circumstances-including the shift of the Fermi (Dirac) points, the change in band gap
of armchair GNRs with uniaxial strain in a zigzag pattern and its insensitivity to shear strain, and the variation of the
k-range of edge states in zigzag GNRs under uniaxial and shear strains which determine the gap behavior via the spin polarization
interaction.
KeywordsGraphene-graphene nanoribbons (GNRs)-band gap-strain-first-principles calculations-tight-binding model
Nano Research 04/2012; 3(8):545-556. · 6.97 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Since the proposal of three-dimensional (3D) domain swapping, many 3D domain-swapped structures have been reported. However, when compared with the vast protein structure space, it is still unclear whether 3D domain swapping is a general mechanism for protein assembly. Here, we investigated this possibility by constructing a dataset consisting of more than 500 domain-swapped structures. The domain-swapped structures were mapped into the protein structure space. We found that about 10% of protein folds and 5% of protein families contain domain-swapped structures. When comparing the domain-swapped structures in a family/superfamily, we found that proteins within a family/superfamily can swap in different ways. Interface analysis revealed that the hinge loops contributed more than half of the open interface in 70% of bona fide domain-swapped dimers, indicating that the hinge loops play an important role in stabilizing the domain-swapped conformations. Our study supports the suggestion that domain swapping is a general property of all proteins and will facilitate further understanding the mechanism of 3D domain swapping.
Proteins Structure Function and Bioinformatics 02/2012; 80(6):1610-9. · 3.39 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The electronic structure of graphene antidot lattices (GALs) with zigzag hole edges was studied with first-principles calculations. It was revealed that half of the possible GAL patterns were unintentionally missed in the usual construction models used in earlier studies. With the complete models, the bandgap of the GALs was sensitive to the width W of the wall between the neighboring holes. A nonzero bandgap was opened in hexagonal GALs with even W, while the bandgap remained closed in those with odd W. Similar alternating gap opening/closing with W was also demonstrated in rhombohedral GALs. Moreover, analytical solutions of single-walled GALs were derived based on a tight-binding model to determine the location of the Dirac points and the energy dispersion, which confirmed the unique effect in GALs.
ACS Nano 05/2011; 5(5):4023-30. · 10.77 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimental discovery of two-state-like folding in the late 1960s, rather than to the problem of conformational search per se. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding, which likely emerges generally from a coupling between local conformational preferences and nonlocal packing interactions. Many of these principles have been elucidated by native-centric models, wherein nonnative interactions may be treated perturbatively. We discuss these developments as well as recent applications of coarse-grained chain modeling to knotted proteins and to intrinsically disordered proteins.
Annual Review of Physical Chemistry 05/2011; 62:301-26. · 14.13 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Anchor residues, which are deeply buried upon binding, play an important role in protein-protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs) which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17-Asn29, abbreviated as p53N) which are involved in binding with two different targets (MDM2 and Taz2), and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex). We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs).
International Journal of Molecular Sciences 01/2011; 12(2):1410-30. · 2.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Intrinsically disordered proteins (IDPs) widely participate in molecular recognition and signaling processes in cells by interacting with other molecules. Compared with ordered proteins, IDPs usually possess stronger intermolecular interactions in binding. As a result, the interface structure of IDPs in complexes is distinct from that of ordered-protein complexes, and this difference may have essential effect on the response to various perturbations in a cell. In this study, we examined the perturbations of intermolecular interactions and temperature on the coupled folding and binding processes of pKID to KIX domains by performing molecular dynamics simulations. By comparing a series of virtual pKID systems with various degree of disorder, we found that the complex stability and the binding kinetics of the disordered systems were less sensitive to the perturbations than the ordered systems. The origin of the lower response sensitivity of IDPs was attributed to their higher flexibility in the complex interface, which was further supported by an analysis on protein complex structures. On the basis of our simulations and results from the literature, we speculate IDPs may not only interact with their biological partners with high specificity and low affinity but also may be resistant to the perturbations in the environment and transmit signals fast and smooth. We proposed to name it the "kinetic buffer" effect.
Proteins Structure Function and Bioinformatics 12/2010; 78(16):3251-9. · 3.39 Impact Factor
-
Journal of Molecular Biology 06/2010; · 4.00 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The mathematical basis of the hypothesis that type-2 topoisomerases recognize and act at specific DNA juxtapositions has been investigated by coarse-grained lattice polymer models, showing that selective segment passages at hooked juxtapositions can result in dramatic reductions in catenane and knot populations. The lattice modeling approach is here extended to account for the narrowing of variance of linking number (Lk) of DNA circles by type-2 topoisomerases. In general, the steady-state variance of Lk resulting from selective segment passages at a specific juxtaposition geometry j is inversely proportional to the average linking number, Lk(j), of circles with the given juxtaposition. Based on this formulation, we demonstrate that selective segment passages at hooked juxtapositions reduce the variance of Lk. The dependence of this effect on model DNA circle size is remarkably similar to that observed experimentally for type-2 topoisomerases, which appear to be less capable in narrowing Lk variance for small DNA circles than for larger DNA circles. This behavior is rationalized by a substantial cancellation of writhe in small circles with hook-like juxtapositions. During our simulations, we uncovered a twisted variation of the hooked juxtaposition that has an even more dramatic effect on Lk variance narrowing than the hooked juxtaposition. For an extended set of juxtapositions, we detected a significant correlation between the Lk narrowing potential and the logarithmic decatenating and unknotting potentials for a given juxtaposition, a trend reminiscent of scaling relations observed with experimental measurements on type-2 topoisomerases from a variety of organisms. The consistent agreement between theory and experiment argues for type-2 topoisomerase action at hooked or twisted-hooked DNA juxtapositions.
Journal of Molecular Biology 05/2010; 400(5):963-82. · 4.00 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: To rationalize the disentangling action of type II topoisomerases, an improved wormlike DNA model was used to delineate the degree of unknotting and decatenating achievable by selective segment passage at specific juxtaposition geometries and to determine how these activities were affected by DNA circle size and solution ionic strength. We found that segment passage at hooked geometries can reduce knot populations as dramatically as seen in experiments. Selective segment passage also provided theoretical underpinning for an intriguing empirical scaling relation between unknotting and decatenating potentials.
Physical Review E 03/2010; 81(3 Pt 1):031902. · 2.26 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Proteins function by interacting with other molecules, where both native and nonnative interactions play important roles. Native interactions contribute to the stability and specificity of a complex, whereas nonnative interactions mainly perturb the binding kinetics. For intrinsically disordered proteins (IDPs), which do not adopt rigid structures when being free in solution, the role of nonnative interactions may be more prominent in binding processes due to their high flexibilities. In this work, we investigated the effect of nonnative hydrophobic interactions on the coupled folding and binding processes of IDPs and its interplay with chain flexibility by conducting molecular dynamics simulations. Our results showed that the free-energy profiles became rugged, and intermediate states occurred when nonnative hydrophobic interactions were introduced. The binding rate was initially accelerated and subsequently dramatically decreased as the strength of the nonnative hydrophobic interactions increased. Both thermodynamic and kinetic analysis showed that disordered systems were more readily affected by nonnative interactions than ordered systems. Furthermore, it was demonstrated that the kinetic advantage of IDPs ("fly-casting" mechanism) was enhanced by nonnative hydrophobic interactions. The relationship between chain flexibility and protein aggregation is also discussed.
PLoS ONE 01/2010; 5(11):e15375. · 4.09 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: betaalphabeta structural motifs are commonly used building blocks in protein structures containing parallel beta-sheets. However, to our knowledge, no stand-alone betaalphabeta structure has been observed in nature to date. Recently, for the first time that we know of, a small protein with an independent betaalphabeta structure (DS119) was successfully designed in our laboratory. To understand the folding mechanism of DS119, in the study described here, we carried out all-atom molecular dynamics and coarse-grained simulations to investigate its folding pathways and energy landscape. From all-atom simulations, we successfully observed the folding event and got a stable folded structure with a minimal root mean-square deviation of 2.6 A with respect to the NMR structure. The folding process can be described as a fast collapse phase followed by rapid formation of the central helix, and then slow formation of a parallel beta-sheet. By using a native-centric Gō-like model, the cooperativity of the system was characterized in terms of the calorimetric criterion, sigmoidal transitions, conformation distribution shifts, and free-energy profiles. DS119 was found to be an incipient downhill folder that folds more cooperatively than a downhill folder, but less cooperatively than a two-state folder. This may reflect the balance between the two structural elements of DS119: the rapidly formed alpha-helix and the slowly formed parallel beta-sheet. Folding times estimated from both the all-atom simulations and the coarse-grained model were at microsecond level, making DS119 another fast folder. Compared to fast folders reported previously, DS119 is, to the best of our knowledge, the first that exhibits a parallel beta-sheet.
Biophysical Journal 01/2010; 98(2):321-9. · 3.65 Impact Factor
