1
|
Xia Y, Xiong Y, Lim B, Skrabalak SE. Shape-controlled synthesis of metal nanocrystals: simple chemistry meets complex physics? Angew Chem Int Ed Engl 2009; 48:60-103. [PMID: 19053095 PMCID: PMC2791829 DOI: 10.1002/anie.200802248] [Citation(s) in RCA: 3133] [Impact Index Per Article: 195.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nanocrystals are fundamental to modern science and technology. Mastery over the shape of a nanocrystal enables control of its properties and enhancement of its usefulness for a given application. Our aim is to present a comprehensive review of current research activities that center on the shape-controlled synthesis of metal nanocrystals. We begin with a brief introduction to nucleation and growth within the context of metal nanocrystal synthesis, followed by a discussion of the possible shapes that a metal nanocrystal might take under different conditions. We then focus on a variety of experimental parameters that have been explored to manipulate the nucleation and growth of metal nanocrystals in solution-phase syntheses in an effort to generate specific shapes. We then elaborate on these approaches by selecting examples in which there is already reasonable understanding for the observed shape control or at least the protocols have proven to be reproducible and controllable. Finally, we highlight a number of applications that have been enabled and/or enhanced by the shape-controlled synthesis of metal nanocrystals. We conclude this article with personal perspectives on the directions toward which future research in this field might take.
Collapse
|
Research Support, N.I.H., Extramural |
16 |
3133 |
2
|
Abstract
As the world's second largest economy, China has experienced severe haze pollution, with fine particulate matter (PM) recently reaching unprecedentedly high levels across many cities, and an understanding of the PM formation mechanism is critical in the development of efficient mediation policies to minimize its regional to global impacts. We demonstrate a periodic cycle of PM episodes in Beijing that is governed by meteorological conditions and characterized by two distinct aerosol formation processes of nucleation and growth, but with a small contribution from primary emissions and regional transport of particles. Nucleation consistently precedes a polluted period, producing a high number concentration of nano-sized particles under clean conditions. Accumulation of the particle mass concentration exceeding several hundred micrograms per cubic meter is accompanied by a continuous size growth from the nucleation-mode particles over multiple days to yield numerous larger particles, distinctive from the aerosol formation typically observed in other regions worldwide. The particle compositions in Beijing, on the other hand, exhibit a similarity to those commonly measured in many global areas, consistent with the chemical constituents dominated by secondary aerosol formation. Our results highlight that regulatory controls of gaseous emissions for volatile organic compounds and nitrogen oxides from local transportation and sulfur dioxide from regional industrial sources represent the key steps to reduce the urban PM level in China.
Collapse
|
Research Support, Non-U.S. Gov't |
11 |
544 |
3
|
Xia Y, Gilroy KD, Peng HC, Xia X. Seed-Mediated Growth of Colloidal Metal Nanocrystals. Angew Chem Int Ed Engl 2016; 56:60-95. [PMID: 27966807 DOI: 10.1002/anie.201604731] [Citation(s) in RCA: 390] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/18/2016] [Indexed: 11/08/2022]
Abstract
Seed-mediated growth is a powerful and versatile approach for the synthesis of colloidal metal nanocrystals. The vast allure of this approach mainly stems from the staggering degree of control one can achieve over the size, shape, composition, and structure of nanocrystals. These parameters not only control the properties of nanocrystals but also determine their relevance to, and performance in, various applications. The ingenuity and artistry inherent to seed-mediated growth offer extensive promise, enhancing a number of existing applications and opening the door to new developments. This Review demonstrates how the diversity of metal nanocrystals can be expanded with endless opportunities by using seeds with well-defined and controllable internal structures in conjunction with a proper combination of capping agent and reduction kinetics. New capabilities and future directions are also highlighted.
Collapse
|
Review |
9 |
390 |
4
|
Hernández-Vega A, Braun M, Scharrel L, Jahnel M, Wegmann S, Hyman BT, Alberti S, Diez S, Hyman AA. Local Nucleation of Microtubule Bundles through Tubulin Concentration into a Condensed Tau Phase. Cell Rep 2018; 20:2304-2312. [PMID: 28877466 PMCID: PMC5828996 DOI: 10.1016/j.celrep.2017.08.042] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/23/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022] Open
Abstract
Non-centrosomal microtubule bundles play important roles in cellular organization and function. Although many diverse proteins are known that can bundle microtubules, biochemical mechanisms by which cells could locally control the nucleation and formation of microtubule bundles are understudied. Here, we demonstrate that the concentration of tubulin into a condensed, liquid-like compartment composed of the unstructured neuronal protein tau is sufficient to nucleate microtubule bundles. We show that, under conditions of macro-molecular crowding, tau forms liquid-like drops. Tubulin partitions into these drops, efficiently increasing tubulin concentration and driving the nucleation of microtubules. These growing microtubules form bundles, which deform the drops while remaining enclosed by diffusible tau molecules exhibiting a liquid-like behavior. Our data suggest that condensed compartments of microtubule bundling proteins could promote the local formation of microtubule bundles in neurons by acting as non-centrosomal microtubule nucleation centers and that liquid-like tau encapsulation could provide both stability and plasticity to long axonal microtubule bundles.
Collapse
|
Journal Article |
7 |
251 |
5
|
Oegema K, Wiese C, Martin OC, Milligan RA, Iwamatsu A, Mitchison TJ, Zheng Y. Characterization of two related Drosophila gamma-tubulin complexes that differ in their ability to nucleate microtubules. J Biophys Biochem Cytol 1999; 144:721-33. [PMID: 10037793 PMCID: PMC2132928 DOI: 10.1083/jcb.144.4.721] [Citation(s) in RCA: 247] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
gamma-tubulin exists in two related complexes in Drosophila embryo extracts (Moritz, M., Y. Zheng, B.M. Alberts, and K. Oegema. 1998. J. Cell Biol. 142:1- 12). Here, we report the purification and characterization of both complexes that we name gamma-tubulin small complex (gammaTuSC; approximately 280,000 D) and Drosophila gammaTuRC ( approximately 2,200,000 D). In addition to gamma-tubulin, the gammaTuSC contains Dgrip84 and Dgrip91, two proteins homologous to the Spc97/98p protein family. The gammaTuSC is a structural subunit of the gammaTuRC, a larger complex containing about six additional polypeptides. Like the gammaTuRC isolated from Xenopus egg extracts (Zheng, Y., M.L. Wong, B. Alberts, and T. Mitchison. 1995. Nature. 378:578-583), the Drosophila gammaTuRC can nucleate microtubules in vitro and has an open ring structure with a diameter of 25 nm. Cryo-electron microscopy reveals a modular structure with approximately 13 radially arranged structural repeats. The gammaTuSC also nucleates microtubules, but much less efficiently than the gammaTuRC, suggesting that assembly into a larger complex enhances nucleating activity. Analysis of the nucleotide content of the gammaTuSC reveals that gamma-tubulin binds preferentially to GDP over GTP, rendering gamma-tubulin an unusual member of the tubulin superfamily.
Collapse
|
research-article |
26 |
247 |
6
|
Yuan C, Levin A, Chen W, Xing R, Zou Q, Herling TW, Challa PK, Knowles TPJ, Yan X. Nucleation and Growth of Amino Acid and Peptide Supramolecular Polymers through Liquid-Liquid Phase Separation. Angew Chem Int Ed Engl 2019; 58:18116-18123. [PMID: 31617663 DOI: 10.1002/anie.201911782] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 12/17/2022]
Abstract
The transition of peptides and proteins from the solution phase into fibrillar structures is a general phenomenon encountered in functional and aberrant biology and is increasingly exploited in soft materials science. However, the fundamental molecular events underpinning the early stages of their assembly and subsequent growth have remained challenging to elucidate. Here, we show that liquid-liquid phase separation into solute-rich and solute-poor phases is a fundamental step leading to the nucleation of supramolecular nanofibrils from molecular building blocks, including peptides and even amphiphilic amino acids. The solute-rich liquid droplets act as nucleation sites, allowing the formation of thermodynamically favorable nanofibrils following Ostwald's step rule. The transition from solution to liquid droplets is entropy driven while the transition from liquid droplets to nanofibrils is mediated by enthalpic interactions and characterized by structural reorganization. These findings shed light on how the nucleation barrier toward the formation of solid phases can be lowered through a kinetic mechanism which proceeds through a metastable liquid phase.
Collapse
|
Research Support, Non-U.S. Gov't |
6 |
244 |
7
|
Abstract
Nearly twenty years ago, Dunitz and Bernstein described a selection of intriguing cases of polymorphs that disappear. The inability to obtain a crystal form that has previously been prepared is indeed a frustrating and potentially serious problem for solid-state scientists. This Review discusses recent occurrences and examples of disappearing polymorphs (as well as the emergence of elusive crystal forms) to demonstrate the enduring relevance of this troublesome, but always captivating, phenomenon in solid-state research. A number of these instances have been central issues in patent litigations. This Review, therefore, also highlights the complex relationship between crystal chemistry and the law.
Collapse
|
review-article |
10 |
199 |
8
|
The Emerging Roles of mTORC1 in Macromanaging Autophagy. Cancers (Basel) 2019; 11:cancers11101422. [PMID: 31554253 PMCID: PMC6826502 DOI: 10.3390/cancers11101422] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 01/18/2023] Open
Abstract
Autophagy is a process of self-degradation that enables the cell to survive when faced with starvation or stressful conditions. The mechanistic target of rapamycin (mTOR), also known as the mammalian target of rapamycin, plays a critical role in maintaining a balance between cellular anabolism and catabolism. mTOR complex 1 (mTORC1) was unveiled as a master regulator of autophagy since inhibition of mTORC1 was required to initiate the autophagy process. Evidence has emerged in recent years to indicate that mTORC1 also directly regulates the subsequent steps of the autophagy process, including the nucleation, autophagosome elongation, autophagosome maturation and termination. By phosphorylating select protein targets of the autophagy core machinery and/or their regulators, mTORC1 can alter their functions, increase their proteasomal degradation or modulate their acetylation status, which is a key switch of the autophagy process. Moreover, it phosphorylates and alters the subcellular localization of transcription factors to suppress the expression of genes needed for autophagosome formation and lysosome biogenesis. The purpose of this review article is to critically analyze current literatures to provide an integrated view of how mTORC1 regulates various steps of the autophagy process.
Collapse
|
Review |
6 |
194 |
9
|
Oksuz O, Narendra V, Lee CH, Descostes N, LeRoy G, Raviram R, Blumenberg L, Karch K, Rocha PP, Garcia BA, Skok JA, Reinberg D. Capturing the Onset of PRC2-Mediated Repressive Domain Formation. Mol Cell 2019; 70:1149-1162.e5. [PMID: 29932905 DOI: 10.1016/j.molcel.2018.05.023] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/10/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022]
Abstract
Polycomb repressive complex 2 (PRC2) maintains gene silencing by catalyzing methylation of histone H3 at lysine 27 (H3K27me2/3) within chromatin. By designing a system whereby PRC2-mediated repressive domains were collapsed and then reconstructed in an inducible fashion in vivo, a two-step mechanism of H3K27me2/3 domain formation became evident. First, PRC2 is stably recruited by the actions of JARID2 and MTF2 to a limited number of spatially interacting "nucleation sites," creating H3K27me3-forming Polycomb foci within the nucleus. Second, PRC2 is allosterically activated via its binding to H3K27me3 and rapidly spreads H3K27me2/3 both in cis and in far-cis via long-range contacts. As PRC2 proceeds further from the nucleation sites, its stability on chromatin decreases such that domains of H3K27me3 remain proximal, and those of H3K27me2 distal, to the nucleation sites. This study demonstrates the principles of de novo establishment of PRC2-mediated repressive domains across the genome.
Collapse
|
Research Support, Non-U.S. Gov't |
6 |
193 |
10
|
Direct calculation of ice homogeneous nucleation rate for a molecular model of water. Proc Natl Acad Sci U S A 2015; 112:10582-8. [PMID: 26240318 DOI: 10.1073/pnas.1509267112] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ice formation is ubiquitous in nature, with important consequences in a variety of environments, including biological cells, soil, aircraft, transportation infrastructure, and atmospheric clouds. However, its intrinsic kinetics and microscopic mechanism are difficult to discern with current experiments. Molecular simulations of ice nucleation are also challenging, and direct rate calculations have only been performed for coarse-grained models of water. For molecular models, only indirect estimates have been obtained, e.g., by assuming the validity of classical nucleation theory. We use a path sampling approach to perform, to our knowledge, the first direct rate calculation of homogeneous nucleation of ice in a molecular model of water. We use TIP4P/Ice, the most accurate among existing molecular models for studying ice polymorphs. By using a novel topological approach to distinguish different polymorphs, we are able to identify a freezing mechanism that involves a competition between cubic and hexagonal ice in the early stages of nucleation. In this competition, the cubic polymorph takes over because the addition of new topological structural motifs consistent with cubic ice leads to the formation of more compact crystallites. This is not true for topological hexagonal motifs, which give rise to elongated crystallites that are not able to grow. This leads to transition states that are rich in cubic ice, and not the thermodynamically stable hexagonal polymorph. This mechanism provides a molecular explanation for the earlier experimental and computational observations of the preference for cubic ice in the literature.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
10 |
169 |
11
|
Makarov DE, Plaxco KW. The topomer search model: A simple, quantitative theory of two-state protein folding kinetics. Protein Sci 2003; 12:17-26. [PMID: 12493824 PMCID: PMC2312397 DOI: 10.1110/ps.0220003] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Most small, single-domain proteins fold with the uncomplicated, single-exponential kinetics expected for diffusion on a smooth energy landscape. Despite this energetic smoothness, the folding rates of these two-state proteins span a remarkable million-fold range. Here, we review the evidence in favor of a simple, mechanistic description, the topomer search model, which quantitatively accounts for the broad scope of observed two-state folding rates. The model, which stipulates that the search for those unfolded conformations with a grossly correct topology is the rate-limiting step in folding, fits observed rates with a correlation coefficient of approximately 0.9 using just two free parameters. The fitted values of these parameters, the pre-exponential attempt frequency and a measure of the difficulty of ordering an unfolded chain, are consistent with previously reported experimental constraints. These results suggest that the topomer search process may dominate the relative barrier heights of two-state protein-folding reactions.
Collapse
|
review-article |
22 |
148 |
12
|
Abstract
Understanding and controlling nucleation is important for many crystallization applications. Calcium carbonate (CaCO3) is often used as a model system to investigate nucleation mechanisms. Despite its great importance in geology, biology, and many industrial applications, CaCO3 nucleation is still a topic of intense discussion, with new pathways for its growth from ions in solution proposed in recent years. These new pathways include the so-called nonclassical nucleation mechanism via the assembly of thermodynamically stable prenucleation clusters, as well as the formation of a dense liquid precursor phase via liquid-liquid phase separation. Here, we present results from a combined experimental and computational investigation on the precipitation of CaCO3 in dilute aqueous solutions. We propose that a dense liquid phase (containing 4-7 H2O per CaCO3 unit) forms in supersaturated solutions through the association of ions and ion pairs without significant participation of larger ion clusters. This liquid acts as the precursor for the formation of solid CaCO3 in the form of vaterite, which grows via a net transfer of ions from solution according to z Ca2+ + z CO32- → z CaCO3 The results show that all steps in this process can be explained according to classical concepts of crystal nucleation and growth, and that long-standing physical concepts of nucleation can describe multistep, multiphase growth mechanisms.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
8 |
133 |
13
|
Ahniyaz A, Sakamoto Y, Bergström L. Magnetic field-induced assembly of oriented superlattices from maghemite nanocubes. Proc Natl Acad Sci U S A 2007; 104:17570-4. [PMID: 17978189 PMCID: PMC2077042 DOI: 10.1073/pnas.0704210104] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2007] [Indexed: 11/18/2022] Open
Abstract
Tailoring the structure of nanocrystal superlattices is an important step toward controlled design of novel nanostructured materials and devices. We demonstrate how the long-range order and macroscopic dimensions of magnetic nanoparticle arrays can be controlled by the use of a modulated magnetic field. Inducing a dipolar attraction during the initial stage of the drying-mediated self-assembly process was sufficient to assemble the superparamagnetic oleate-capped maghemite nanocubes into large and defect-free superstructures with both translational and orientational order. The characteristic dimensions of the superlattice are controlled by the particle concentration as well as the duration of the applied magnetic field. The superparamagnetic maghemite nanocubes assemble into large and highly oriented thin arrays by applying the magnetic field perpendicular to the substrate surface only during the initial phase of drying-mediated self-assembly. Micrometer-sized and thick three-dimensional mesocrystals are obtained when the drying dispersion is subjected to an external magnetic field of moderate strength for the entire duration of the assembly process. The discovery of how translational and orientation order of nanocrystal superlattices can be induced by a temporal modulation of an anisotropic interparticle force offers new insight on the importance of the initial nucleation stage in the self-assembly process and suggests new routes for controlled self-assembly of dipolar nanocrystals.
Collapse
|
research-article |
18 |
132 |
14
|
Chen Q, Luo L, Faraji H, Feldberg SW, White HS. Electrochemical Measurements of Single H2 Nanobubble Nucleation and Stability at Pt Nanoelectrodes. J Phys Chem Lett 2014; 5:3539-44. [PMID: 26278606 DOI: 10.1021/jz501898r] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Single H2 nanobubble nucleation is studied at Pt nanodisk electrodes of radii less than 50 nm, where H2 is produced through electrochemical reduction of protons in a strong acid solution. The critical concentration of dissolved H2 required for nanobubble nucleation is measured to be ∼0.25 M. This value is ∼310 times larger than the saturation concentration at room temperature and pressure and was found to be independent of acid type (e.g., H2SO4, HCl, and H3PO4) and nanoelectrode size. The effects of different surfactants on H2 nanobubble nucleation are consistent with the classic nucleation theory. As the surfactant concentration in H2SO4 solution increases, the solution surface tension decreases, resulting in a lower nucleation energy barrier and consequently a lower supersaturation concentration required for H2 nanobubble nucleation. Furthermore, amphiphilic surfactant molecules accumulate at the H2/solution interface, hindering interfacial H2 transfer from the nanobubble into the solution; consequently, the residual current decreases with increasing surfactant concentration.
Collapse
|
|
11 |
117 |
15
|
McMeekin DP, Wang Z, Rehman W, Pulvirenti F, Patel JB, Noel NK, Johnston MB, Marder SR, Herz LM, Snaith HJ. Crystallization Kinetics and Morphology Control of Formamidinium-Cesium Mixed-Cation Lead Mixed-Halide Perovskite via Tunability of the Colloidal Precursor Solution. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29. [PMID: 28561912 DOI: 10.1002/adma.201607039] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/06/2017] [Indexed: 05/11/2023]
Abstract
The meteoric rise of the field of perovskite solar cells has been fueled by the ease with which a wide range of high-quality materials can be fabricated via simple solution processing methods. However, to date, little effort has been devoted to understanding the precursor solutions, and the role of additives such as hydrohalic acids upon film crystallization and final optoelectronic quality. Here, a direct link between the colloids concentration present in the [HC(NH2 )2 ]0.83 Cs0.17 Pb(Br0.2 I0.8 )3 precursor solution and the nucleation and growth stages of the thin film formation is established. Using dynamic light scattering analysis, the dissolution of colloids over a time span triggered by the addition of hydrohalic acids is monitored. These colloids appear to provide nucleation sites for the perovskite crystallization, which critically impacts morphology, crystal quality, and optoelectronic properties. Via 2D X-ray diffraction, highly ordered and textured crystals for films prepared from solutions with lower colloidal concentrations are observed. This increase in material quality allows for a reduction in microstrain along with a twofold increase in charge-carrier mobilities leading to values exceeding 20 cm2 V-1 s-1 . Using a solution with an optimized colloidal concentration, devices that reach current-voltage measured power conversion efficiency of 18.8% and stabilized efficiency of 17.9% are fabricated.
Collapse
|
|
8 |
110 |
16
|
Yang C, Huang M, DeBiasio J, Pring M, Joyce M, Miki H, Takenawa T, Zigmond SH. Profilin enhances Cdc42-induced nucleation of actin polymerization. J Cell Biol 2000; 150:1001-12. [PMID: 10973991 PMCID: PMC2175244 DOI: 10.1083/jcb.150.5.1001] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We find that profilin contributes in several ways to Cdc42-induced nucleation of actin filaments in high speed supernatant of lysed neutrophils. Depletion of profilin inhibited Cdc42-induced nucleation; re-addition of profilin restored much of the activity. Mutant profilins with a decreased affinity for either actin or poly-l-proline were less effective at restoring activity. Whereas Cdc42 must activate Wiskott-Aldrich Syndrome protein (WASP) to stimulate nucleation by the Arp2/3 complex, VCA (verpolin homology, cofilin, and acidic domain contained in the COOH-terminal fragment of N-WASP) constitutively activates the Arp2/3 complex. Nucleation by VCA was not inhibited by profilin depletion. With purified N-WASP and Arp2/3 complex, Cdc42-induced nucleation did not require profilin but was enhanced by profilin, wild-type profilin being more effective than mutant profilin with reduced affinity for poly-l-proline. Nucleation by the Arp2/3 complex is a function of the free G-actin concentration. Thus, when profilin addition decreased the free G-actin concentration, it inhibited Cdc42- and VCA-induced nucleation. However, when profilin was added with G-actin in a ratio that maintained the initial free G-actin concentration, it increased the rate of both Cdc42- and VCA-induced nucleation. This enhancement, also seen with purified proteins, was greatest when the free G-actin concentration was low. These data suggest that under conditions present in intact cells, profilin enhances nucleation by activated Arp2/3 complex.
Collapse
|
research-article |
25 |
108 |
17
|
Exploring the aggregation free energy landscape of the amyloid-β protein (1-40). Proc Natl Acad Sci U S A 2016; 113:11835-11840. [PMID: 27698130 DOI: 10.1073/pnas.1612362113] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A predictive coarse-grained protein force field [associative memory, water-mediated, structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the energy landscapes and relative stabilities of amyloid-β protein (1-40) in the monomer and all of its oligomeric forms up to an octamer. We find that an isolated monomer is mainly disordered with a short α-helix formed at the central hydrophobic core region (L17-D23). A less stable hairpin structure, however, becomes increasingly more stable in oligomers, where hydrogen bonds can form between neighboring monomers. We explore the structure and stability of both prefibrillar oligomers that consist of mainly antiparallel β-sheets and fibrillar oligomers with only parallel β-sheets. Prefibrillar oligomers are polymorphic but typically take on a cylindrin-like shape composed of mostly antiparallel β-strands. At the concentration of the simulation, the aggregation free energy landscape is nearly downhill. We use umbrella sampling along a structural progress coordinate for interconversion between prefibrillar and fibrillar forms to identify a conversion pathway between these forms. The fibrillar oligomer only becomes favored over its prefibrillar counterpart in the pentamer where an interconversion bottleneck appears. The structural characterization of the pathway along with statistical mechanical perturbation theory allow us to evaluate the effects of concentration on the free energy landscape of aggregation as well as the effects of the Dutch and Arctic mutations associated with early onset of Alzheimer's disease.
Collapse
|
Research Support, Non-U.S. Gov't |
9 |
103 |
18
|
Abstract
Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.
Collapse
|
Research Support, Non-U.S. Gov't |
11 |
99 |
19
|
Chen XR, Zhao BC, Yan C, Zhang Q. Review on Li Deposition in Working Batteries: From Nucleation to Early Growth. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2004128. [PMID: 33432664 DOI: 10.1002/adma.202004128] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/19/2020] [Indexed: 06/12/2023]
Abstract
Lithium (Li) metal is one of the most promising alternative anode materials of next-generation high-energy-density batteries demanded for advanced energy storage in the coming fourth industrial revolution. Nevertheless, disordered Li deposition easily causes short lifespan and safety concerns and thus severely hinders the practical applications of Li metal batteries. Tremendous efforts are devoted to understanding the mechanism for Li deposition, while the final deposition morphology tightly relies on the Li nucleation and early growth. Here, the recent progress in insightful and influential models proposed to understand the process of Li deposition from nucleation to early growth, including the heterogeneous model, surface diffusion model, crystallography model, space charge model, and Li-SEI model, are highlighted. Inspired by the abovementioned understanding on Li nucleation and early growth, diverse anode-design strategies, which contribute to better batteries with superior electrochemical performance and dendrite-free deposition behavior, are also summarized. This work broadens the horizon for practical Li metal batteries and also sheds light on more understanding of other important metal-based batteries involving the metal deposition process.
Collapse
|
Review |
4 |
99 |
20
|
Borreguero JM, Urbanc B, Lazo ND, Buldyrev SV, Teplow DB, Stanley HE. Folding events in the 21-30 region of amyloid beta-protein (Abeta) studied in silico. Proc Natl Acad Sci U S A 2005; 102:6015-20. [PMID: 15837927 PMCID: PMC1087952 DOI: 10.1073/pnas.0502006102] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Oligomeric assemblies of the amyloid beta-protein (Abeta) have been implicated in the pathogenesis of Alzheimer's disease as a primary source of neurotoxicity. Recent in vitro studies have suggested that a 10-residue segment, Ala-21-Ala-30, forms a turn-like structure that nucleates the folding of the full-length Abeta. To gain a mechanistic insight, we simulated Abeta(21-30) folding by using a discrete molecular dynamics algorithm and a united-atom model incorporating implicit solvent and a variable electrostatic interaction strength (EIS). We found that Abeta(21-30) folds into a loop-like conformation driven by an effective hydrophobic attraction between Val-24 and the butyl portion of the Lys-28 side chain. At medium EIS [1.5 kcal/mol (1 cal = 4.18 J)], unfolded conformations almost disappear, in agreement with experimental observations. Under optimal conditions for folding, Glu-22 and Asp-23 form transient electrostatic interactions (EI) with Lys-28 that stabilize the loop conformations. Glu-22-Lys-28 is the most favored interaction. High EIS, as it occurs in the interior of proteins and aggregates, destabilizes the packing of Val-24 and Lys-28. Analysis of the unpacked structures reveals strong EI with predominance of the Asp-23-Lys-28 interaction, in agreement with studies of molecular modeling of full-length Abeta fibrils. The binary nature of the EI involving Lys-28 provides a mechanistic explanation for the linkage of amino acid substitutions at Glu-22 with Alzheimer's disease and cerebral amyloid angiopathy. Substitutions may alter the frequency of Glu-22 or Asp-23 involvement in contact formation and affect the stability of the folding nucleus formed in the Abeta(21-30) region.
Collapse
|
Research Support, N.I.H., Extramural |
20 |
98 |
21
|
Nölting B, Golbik R, Neira JL, Soler-Gonzalez AS, Schreiber G, Fersht AR. The folding pathway of a protein at high resolution from microseconds to seconds. Proc Natl Acad Sci U S A 1997; 94:826-30. [PMID: 9023341 PMCID: PMC19598 DOI: 10.1073/pnas.94.3.826] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have documented the folding pathway of the 10-kDa protein barstar from the first few microseconds at the resolution of individual residues from its well characterized denatured state. The denatured state had been shown from NMR to have flickering native-like structure in the first two of its four alpha-helices. phi-value analysis shows that the first helix becomes substantially consolidated as the intermediate is formed in a few hundred microseconds, as does the second to a lesser extent. A native-like structure then is formed in a few hundred milliseconds as the whole structure consolidates. Peptide fragments corresponding to sequences containing the first two helices separately and together as a helix-loop-helix motif have little helical structure under conditions that favor folding. The early stages of folding fit the nucleation-condensation model that was proposed for the smaller chymotrypsin inhibitor 2, which is a single module of structure and folds by two-state kinetics. The early stages of the multistate folding of the larger, multimodular, barnase have proved experimentally inaccessible. The folding pathway of barstar links those of CI2 and barnase to give a unified scheme for folding.
Collapse
|
research-article |
28 |
96 |
22
|
Abstract
Nucleation, the primary step in crystallization, dictates the number of crystals, the distribution of their sizes, the polymorph selection, and other crucial properties of the crystal population. We used time-resolved liquid-cell transmission electron microscopy (TEM) to perform an in situ examination of the nucleation of lysozyme crystals. Our TEM images revealed that mesoscopic clusters, which are similar to those previously assumed to consist of a dense liquid and serve as nucleation precursors, are actually amorphous solid particles (ASPs) and act only as heterogeneous nucleation sites. Crystalline phases never form inside them. We demonstrate that a crystal appears within a noncrystalline particle assembling lysozyme on an ASP or a container wall, highlighting the role of heterogeneous nucleation. These findings represent a significant departure from the existing formulation of the two-step nucleation mechanism while reaffirming the role of noncrystalline particles. The insights gained may have significant implications in areas that rely on the production of protein crystals, such as structural biology, pharmacy, and biophysics, and for the fundamental understanding of crystallization mechanisms.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
8 |
95 |
23
|
Gribaudo S, Tixador P, Bousset L, Fenyi A, Lino P, Melki R, Peyrin JM, Perrier AL. Propagation of α-Synuclein Strains within Human Reconstructed Neuronal Network. Stem Cell Reports 2019; 12:230-244. [PMID: 30639210 PMCID: PMC6372945 DOI: 10.1016/j.stemcr.2018.12.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
Reappraisal of neuropathological studies suggests that pathological hallmarks of Alzheimer’s disease and Parkinson’s disease (PD) spread progressively along predictable neuronal pathways in the human brain through unknown mechanisms. Although there is much evidence supporting the prion-like propagation and amplification of α-synuclein (α-Syn) in vitro and in rodent models, whether this scenario occurs in the human brain remains to be substantiated. Here we reconstructed in microfluidic devices corticocortical neuronal networks using human induced pluripotent stem cells derived from a healthy donor. We provide unique experimental evidence that different strains of human α-Syn disseminate in “wild-type” human neuronal networks in a prion-like manner. We show that two distinct α-Syn strains we named fibrils and ribbons are transported, traffic between neurons, and trigger to different extents, in a dose- and structure-dependent manner, the progressive accumulation of PD-like pathological hallmarks. We further demonstrate that seeded aggregation of endogenous soluble α-Syn affects synaptic integrity and mitochondria morphology.
Different α-Syn strains propagate within WT human iPSC-derived cortical neuronal networks α-Syn strains differentially seed endogenous WT α-Syn forming LB/LN-like structures Phospho-α-Syn endogenous aggregates resist degradation and accumulate in cytoplasm Accumulation of phospho-α-Syn induces early neuronal dysfunctions
Collapse
|
Research Support, Non-U.S. Gov't |
6 |
95 |
24
|
Abstract
Microtubules (MTs) form a rapidly adaptable network of filaments that radiate throughout the cell. These dynamic arrays facilitate a wide range of cellular processes, including the capture, transport, and spatial organization of cargos and organelles, as well as changes in cell shape, polarity, and motility. Nucleating from MT-organizing centers, including but by no means limited to the centrosome, MTs undergo rapid transitions through phases of growth, pause, and catastrophe, continuously exploring and adapting to the intracellular environment. Subsets of MTs can become stabilized in response to environmental cues, acquiring distinguishing posttranslational modifications and performing discrete functions as specialized tracks for cargo trafficking. The dynamic behavior and organization of the MT array is regulated by MT-associated proteins (MAPs), which include a subset of highly specialized plus-end-tracking proteins (+TIPs) that respond to signaling cues to alter MT behavior. As pathogenic cargos, viruses require MTs to transport to and from their intracellular sites of replication. While interactions with and functions for MT motor proteins are well characterized and extensively reviewed for many viruses, this review focuses on MT filaments themselves. Changes in the spatial organization and dynamics of the MT array, mediated by virus- or host-induced changes to MT regulatory proteins, not only play a central role in the intracellular transport of virus particles but also regulate a wider range of processes critical to the outcome of infection.
Collapse
|
Research Support, N.I.H., Extramural |
8 |
91 |
25
|
Evaporation-triggered microdroplet nucleation and the four life phases of an evaporating Ouzo drop. Proc Natl Acad Sci U S A 2016; 113:8642-7. [PMID: 27418601 DOI: 10.1073/pnas.1602260113] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evaporating liquid droplets are omnipresent in nature and technology, such as in inkjet printing, coating, deposition of materials, medical diagnostics, agriculture, the food industry, cosmetics, or spills of liquids. Whereas the evaporation of pure liquids, liquids with dispersed particles, or even liquid mixtures has intensively been studied over the past two decades, the evaporation of ternary mixtures of liquids with different volatilities and mutual solubilities has not yet been explored. Here we show that the evaporation of such ternary mixtures can trigger a phase transition and the nucleation of microdroplets of one of the components of the mixture. As a model system, we pick a sessile Ouzo droplet (as known from daily life-a transparent mixture of water, ethanol, and anise oil) and reveal and theoretically explain its four life phases: In phase I, the spherical cap-shaped droplet remains transparent while the more volatile ethanol is evaporating, preferentially at the rim of the drop because of the singularity there. This leads to a local ethanol concentration reduction and correspondingly to oil droplet nucleation there. This is the beginning of phase II, in which oil microdroplets quickly nucleate in the whole drop, leading to its milky color that typifies the so-called "Ouzo effect." Once all ethanol has evaporated, the drop, which now has a characteristic nonspherical cap shape, has become clear again, with a water drop sitting on an oil ring (phase III), finalizing the phase inversion. Finally, in phase IV, all water has evaporated, leaving behind a tiny spherical cap-shaped oil drop.
Collapse
|
Research Support, Non-U.S. Gov't |
9 |
90 |