共查询到20条相似文献，搜索用时 46 毫秒
1.
King NP Sheffler W Sawaya MR Vollmar BS Sumida JP André I Gonen T Yeates TO Baker D 《Science (New York, N.Y.)》2012,336(6085):1171-1174
We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials. 相似文献
2.
Lange OF Lakomek NA Farès C Schröder GF Walter KF Becker S Meiler J Grubmüller H Griesinger C de Groot BL 《Science (New York, N.Y.)》2008,320(5882):1471-1475
Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost. 相似文献
3.
Schotte F Lim M Jackson TA Smirnov AV Soman J Olson JS Phillips GN Wulff M Anfinrud PA 《Science (New York, N.Y.)》2003,300(5627):1944-1947
We report picosecond time-resolved x-ray diffraction from the myoglobin (Mb) mutant in which Leu29 is replaced by Phe (L29Fmutant). The frame-by-frame structural evolution, resolved to 1.8 angstroms, allows one to literally "watch" the protein as it executes its function. Time-resolved mid-infrared spectroscopy of flash-photolyzed L29F MbCO revealed a short-lived CO intermediate whose 140-ps lifetime is shorter than that found in wild-type protein by a factor of 1000. The electron density maps of the protein unveil transient conformational changes far more dramatic than the structural differences between the carboxy and deoxy states and depict the correlated side-chain motion responsible for rapidly sweeping CO away from its primary docking site. 相似文献
4.
Mikosch J Trippel S Eichhorn C Otto R Lourderaj U Zhang JX Hase WL Weidemüller M Wester R 《Science (New York, N.Y.)》2008,319(5860):183-186
Anion-molecule nucleophilic substitution (S(N)2) reactions are known for their rich reaction dynamics, caused by a complex potential energy surface with a submerged barrier and by weak coupling of the relevant rotational-vibrational quantum states. The dynamics of the S(N)2 reaction of Cl- + CH3I were uncovered in detail by using crossed molecular beam imaging. As a function of the collision energy, the transition from a complex-mediated reaction mechanism to direct backward scattering of the I- product was observed experimentally. Chemical dynamics calculations were performed that explain the observed energy transfer and reveal an indirect roundabout reaction mechanism involving CH3 rotation. 相似文献
5.
Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation of the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized the motions of NtrC in three functional states: unphosphorylated (inactive), phosphorylated (active), and a partially active mutant. These dynamics are indicative of exchange between inactive and active conformations. Both states are populated in unphosphorylated NtrC, and phosphorylation shifts the equilibrium toward the active species. These results support a dynamic population shift between two preexisting conformations as the underlying mechanism of activation. 相似文献
6.
A critical role is traditionally assigned to transition states (TSs) and minimum energy pathways, or intrinsic reaction coordinates (IRCs), in interpreting organic reactivity. Such an interpretation, however, ignores vibrational and kinetic energy effects of finite temperature. Recently it has been shown that reactions do not necessarily follow the intermediates along the IRC. We report here molecular dynamics (MD) simulations that show that dynamics effects may alter chemical reactions even more. In the heterolysis rearrangement of protonated pinacolyl alcohol Me3C-CHMe-OH2+ (Me, methyl), the MD pathway involves a stepwise route with C-O bond cleavage followed by methyl group migration, whereas the IRC pathway suggests a concerted mechanism. Dynamics effects may lead to new interpretations of organic reactivity. 相似文献
7.
Berthe M Stiufiuc R Grandidier B Deresmes D Delerue C Stiévenard D 《Science (New York, N.Y.)》2008,319(5862):436-438
The performance of many semiconductor quantum-based structures is governed by the dynamics of charge carriers between a localized state and a band of electronic states. Using scanning tunneling spectroscopy, we studied the transport of inelastic tunneling electrons through a prototypical localized state: an isolated dangling-bond state on a Si(111) surface. From the saturation of the current at an energy resonant with this state, the hole capture rate by the dangling bond was determined. By further mapping the spatial extension of its wave function, the localized nature of the level was found to be consistent with the small magnitude of its cross section. This approach illustrates how the microscopic environment of a single defect critically affects its carrier dynamics. 相似文献
8.
Bayer M Hawrylak P Hinzer K Fafard S Korkusinski M Wasilewski ZR Stern O Forchel A 《Science (New York, N.Y.)》2001,291(5503):451-453
We demonstrate coupling and entangling of quantum states in a pair of vertically aligned, self-assembled quantum dots by studying the emission of an interacting electron-hole pair (exciton) in a single dot molecule as a function of the separation between the dots. An interaction-induced energy splitting of the exciton is observed that exceeds 30 millielectron volts for a dot layer separation of 4 nanometers. The results are interpreted by mapping the tunneling of a particle in a double dot to the problem of a single spin. The electron-hole complex is shown to be equivalent to entangled states of two interacting spins. 相似文献
9.
Wu CC Li TK Farh L Lin LY Lin TS Yu YJ Yen TJ Chiang CW Chan NL 《Science (New York, N.Y.)》2011,333(6041):459-462
Type II topoisomerases (TOP2s) resolve the topological problems of DNA by transiently cleaving both strands of a DNA duplex to form a cleavage complex through which another DNA segment can be transported. Several widely prescribed anticancer drugs increase the population of TOP2 cleavage complex, which leads to TOP2-mediated chromosome DNA breakage and death of cancer cells. We present the crystal structure of a large fragment of human TOP2β complexed to DNA and to the anticancer drug etoposide to reveal structural details of drug-induced stabilization of a cleavage complex. The interplay between the protein, the DNA, and the drug explains the structure-activity relations of etoposide derivatives and the molecular basis of drug-resistant mutations. The analysis of protein-drug interactions provides information applicable for developing an isoform-specific TOP2-targeting strategy. 相似文献
10.
Rosenfeld DE Gengeliczki Z Smith BJ Stack TD Fayer MD 《Science (New York, N.Y.)》2011,334(6056):634-639
Ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy has proven broadly useful for studying molecular dynamics in solutions. Here, we extend the technique to probing the interfacial dynamics and structure of a silica surface-tethered transition metal carbonyl complex--tricarbonyl (1,10-phenanthroline)rhenium chloride--of interest as a photoreduction catalyst. We interpret the data using a theoretical framework devised to separate the roles of structural evolution and excitation transfer in inducing spectral diffusion. The structural dynamics, as reported on by a carbonyl stretch vibration of the surface-bound complex, have a characteristic time of ~150 picoseconds in the absence of solvent, decrease in duration by a factor of three upon addition of chloroform, and decrease another order of magnitude for the bulk solution. Conversely, solvent-complex interactions increase the lifetime of the probed vibration by 160% when solvent is applied to the monolayer. 相似文献
11.
Pham KN Puertas AM Bergenholtz J Egelhaaf SU Moussaïd A Pusey PN Schofield AB Cates ME Fuchs M Poon WC 《Science (New York, N.Y.)》2002,296(5565):104-106
Experiments, theory, and simulation were used to study glass formation in a simple model system composed of hard spheres with short-range attraction ("sticky hard spheres"). The experiments, using well-characterized colloids, revealed a reentrant glass transition line. Mode-coupling theory calculations and molecular dynamics simulations suggest that the reentrance is due to the existence of two qualitatively different glassy states: one dominated by repulsion (with structural arrest due to caging) and the other by attraction (with structural arrest due to bonding). This picture is consistent with a study of the particle dynamics in the colloid using dynamic light scattering. 相似文献
12.
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters convert chemical energy from ATP hydrolysis to mechanical work for substrate translocation. They function by alternating between two states, exposing the substrate-binding site to either side of the membrane. A key question that remains to be addressed is how substrates initiate the transport cycle. Using x-ray crystallography, we have captured the maltose transporter in an intermediate step between the inward- and outward-facing states. We show that interactions with substrate-loaded maltose-binding protein in the periplasm induce a partial closure of the MalK dimer in the cytoplasm. ATP binding to this conformation then promotes progression to the outward-facing state. These results, interpreted in light of biochemical and functional studies, provide a structural basis to understand allosteric communication in ABC transporters. 相似文献
13.
We present experimental evidence, obtained from small-angle neutron scattering and photon correlation measurements, indicating the existence of two types of structurally arrested (glassy) states in a copolymer micellar system with a short-range interparticle attractive interaction. Within a certain range of micellar volume fractions, a sharp transition between these two types of glass is observed by varying the temperature. Furthermore, we found an end point of this transition line beyond which the two glasses become identical in their local structure and their long-time dynamics. These findings confirm the recent mode-coupling theory predictions regarding the phase behavior of the structurally arrested states for this type of system. 相似文献
14.
Neuronal networks in vivo are characterized by considerable spontaneous activity, which is highly complex and intrinsically generated by a combination of single-cell electrophysiological properties and recurrent circuits. As seen, for example, during waking compared with being asleep or under anesthesia, neuronal responsiveness differs, concomitant with the pattern of spontaneous brain activity. This pattern, which defines the state of the network, has a dramatic influence on how local networks are engaged by inputs and, therefore, on how information is represented. We review here experimental and theoretical evidence of the decisive role played by stochastic network states in sensory responsiveness with emphasis on activated states such as waking. From single cells to networks, experiments and computational models have addressed the relation between neuronal responsiveness and the complex spatiotemporal patterns of network activity. The understanding of the relation between network state dynamics and information representation is a major challenge that will require developing, in conjunction, specific experimental paradigms and theoretical frameworks. 相似文献
15.
The most common catalyst in the Haber-Bosch process for the hydrogenation of dinitrogen (N(2)) to ammonia (NH(3)) is an iron surface promoted with potassium cations (K(+)), but soluble iron complexes have neither reduced the N-N bond of N(2) to nitride (N(3-)) nor produced large amounts of NH(3) from N(2). We report a molecular iron complex that reacts with N(2) and a potassium reductant to give a complex with two nitrides, which are bound to iron and potassium cations. The product has a Fe(3)N(2) core, implying that three iron atoms cooperate to break the N-N triple bond through a six-electron reduction. The nitride complex reacts with acid and with H(2) to give substantial yields of N(2)-derived ammonia. These reactions, although not yet catalytic, give structural and spectroscopic insight into N(2) cleavage and N-H bond-forming reactions of iron. 相似文献
16.
Yu IM Zhang W Holdaway HA Li L Kostyuchenko VA Chipman PR Kuhn RJ Rossmann MG Chen J 《Science (New York, N.Y.)》2008,319(5871):1834-1837
Intracellular cleavage of immature flaviviruses is a critical step in assembly that generates the membrane fusion potential of the E glycoprotein. With cryo-electron microscopy we show that the immature dengue particles undergo a reversible conformational change at low pH that renders them accessible to furin cleavage. At a pH of 6.0, the E proteins are arranged in a herringbone pattern with the pr peptides docked onto the fusion loops, a configuration similar to that of the mature virion. After cleavage, the dissociation of pr is pH-dependent, suggesting that in the acidic environment of the trans-Golgi network pr is retained on the virion to prevent membrane fusion. These results suggest a mechanism by which flaviviruses are processed and stabilized in the host cell secretory pathway. 相似文献
17.
We directly observed the hydration dynamics of an excess electron in the finite-sized water clusters of (H2O)n- with n = 15, 20, 25, 30, and 35. We initiated the solvent motion by exciting the hydrated electron in the cluster. By resolving the binding energy of the excess electron in real time with femtosecond resolution, we captured the ultrafast dynamics of the electron in the presolvated ("wet") and hydrated states and obtained, as a function of cluster size, the subsequent relaxation times. The solvation time (300 femtoseconds) after the internal conversion [140 femtoseconds for (H2O)35-] was similar to that of bulk water, indicating the dominant role of the local water structure in the dynamics of hydration. In contrast, the relaxation in other nuclear coordinates was on a much longer time scale (2 to 10 picoseconds) and depended critically on cluster size. 相似文献
18.
Barnett RN Cleveland CL Joy A Landman U Schuster GB 《Science (New York, N.Y.)》2001,294(5542):567-571
Electron hole (radical cation) migration in DNA, where the quantum transport of an injected charge is gated in a correlated manner by the thermal motions of the hydrated counterions, is described here. Classical molecular dynamics simulations in conjunction with large-scale first-principles electronic structure calculations reveal that different counterion configurations lead to formation of states characterized by varying spatial distributions and degrees of charge localization. Stochastic dynamic fluctuations between such ionic configurations can induce correlated changes in the spatial distribution of the hole, with concomitant transport along the DNA double helix. Comparative ultraviolet light-induced cleavage experiments on native B DNA oligomers and on ones modified to contain counterion (Na(+))-starved bridges between damage-susceptible hole-trapping sites called GG steps show in the latter a reduction in damage at the distal step. This reduction indicates a reduced mobility of the hole across the modified bridge as predicted theoretically. 相似文献
19.
Henson SM Costantino RF Cushing JM Desharnais RA Dennis B King AA 《Science (New York, N.Y.)》2001,294(5542):602-605
Animals and many plants are counted in discrete units. The collection of possible values (state space) of population numbers is thus a nonnegative integer lattice. Despite this fact, many mathematical population models assume a continuum of system states. The complex dynamics, such as chaos, often displayed by such continuous-state models have stimulated much ecological research; yet discrete-state models with bounded population size can display only cyclic behavior. Motivated by data from a population experiment, we compared the predictions of discrete-state and continuous-state population models. Neither the discrete- nor continuous-state models completely account for the data. Rather, the observed dynamics are explained by a stochastic blending of the chaotic dynamics predicted by the continuous-state model and the cyclic dynamics predicted by the discrete-state models. We suggest that such lattice effects could be an important component of natural population fluctuations. 相似文献
20.
Gregoryanz E Lundegaard LF McMahon MI Guillaume C Nelmes RJ Mezouar M 《Science (New York, N.Y.)》2008,320(5879):1054-1057
Sodium exhibits a pronounced minimum of the melting temperature at approximately 118 gigapascals and 300 kelvin. Using single-crystal high-pressure diffraction techniques, we found that the minimum of the sodium melting curve is associated with a concentration of seven different crystalline phases. Slight changes in pressure and/or temperature induce transitions between numerous structural modifications, several of which are highly complex. The complexity of the phase behavior above 100 gigapascals suggests extraordinary liquid and solid states of sodium at extreme conditions and has implications for other seemingly simple metals. 相似文献