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1.
Proc Natl Acad Sci U S A ; 113(10): 2591-6, 2016 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-26903637

RESUMO

The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

2.
Biophys J ; 111(7): 1465-1477, 2016 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-27705769

RESUMO

Actin filaments have key roles in cell motility but are generally claimed to be passive interaction partners in actin-myosin-based motion generation. Here, we present evidence against this static view based on an altered myosin-induced actin filament gliding pattern in an in vitro motility assay at varied [MgATP]. The statistics that characterize the degree of meandering of the actin filament paths suggest that for [MgATP] ≥ 0.25 mM, the flexural rigidity of heavy meromyosin (HMM)-propelled actin filaments is similar (without phalloidin) or slightly lower (with phalloidin) than that of HMM-free filaments observed in solution without surface tethering. When [MgATP] was reduced to ≤0.1 mM, the actin filament paths in the in vitro motility assay became appreciably more winding in both the presence and absence of phalloidin. This effect of lowered [MgATP] was qualitatively different from that seen when HMM was mixed with ATP-insensitive, N-ethylmaleimide-treated HMM (NEM-HMM; 25-30%). In particular, the addition of NEM-HMM increased a non-Gaussian tail in the path curvature distribution as well as the number of events in which different parts of an actin filament followed different paths. These effects were the opposite of those observed with reduced [MgATP]. Theoretical modeling suggests a 30-40% lowered flexural rigidity of the actin filaments at [MgATP] ≤ 0.1 mM and local bending of the filament front upon each myosin head attachment. Overall, the results fit with appreciable structural changes in the actin filament during actomyosin-based motion generation, and modulation of the actin filament mechanical properties by the dominating chemomechanical actomyosin state.


Assuntos
Citoesqueleto de Actina/química , Trifosfato de Adenosina/química , Subfragmentos de Miosina/química , Citoesqueleto de Actina/metabolismo , Trifosfato de Adenosina/metabolismo , Animais , Transporte Biológico , Elasticidade , Modelos Moleculares , Músculo Esquelético/química , Músculo Esquelético/metabolismo , Subfragmentos de Miosina/metabolismo , Dinâmica não Linear , Faloidina/química , Conformação Proteica , Soluções/química
3.
Biochim Biophys Acta ; 1840(6): 1933-42, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24418515

RESUMO

BACKGROUND: Bundles of unipolar actin filaments (F-actin), cross-linked via the actin-binding protein fascin, are important in filopodia of motile cells and stereocilia of inner ear sensory cells. However, such bundles are also useful as shuttles in myosin-driven nanotechnological applications. Therefore, and for elucidating aspects of biological function, we investigate if the bundle tendency to follow straight paths (quantified by path persistence length) when propelled by myosin motors is directly determined by material properties quantified by persistence length of thermally fluctuating bundles. METHODS: Fluorescent bundles, labeled with rhodamine-phalloidin, were studied at fascin:actin molar ratios: 0:1 (F-actin), 1:7, 1:4 and 1:2. Persistence lengths (Lp) were obtained by fitting the cosine correlation function (CCF) to a single exponential function: =exp(-s/(2Lp)) where θ(s) is tangent angle; s: path or contour lengths. < > denotes averaging over filaments. RESULTS: Bundle-Lp (bundles<15µm long) increased from ~10 to 150µm with increased fascin:actin ratio. The increase was similar for path-Lp (path<15µm), with highly linear correlation. For longer bundle paths, the CCF-decay deviated from a single exponential, consistent with superimposition of the random path with a circular path as suggested by theoretical analysis. CONCLUSIONS: Fascin-actin bundles have similar path-Lp and bundle-Lp, both increasing with fascin:actin ratio. Path-Lp is determined by the flexural rigidity of the bundle. GENERAL SIGNIFICANCE: The findings give general insight into mechanics of cytoskeletal polymers that interact with molecular motors, aid rational development of nanotechnological applications and have implications for structure and in vivo functions of fascin-actin bundles.


Assuntos
Citoesqueleto de Actina/química , Citoesqueleto de Actina/fisiologia , Proteínas de Transporte/química , Proteínas dos Microfilamentos/química , Proteínas de Transporte/fisiologia , Proteínas dos Microfilamentos/fisiologia , Movimento , Nanotecnologia , Soluções
5.
Biophys J ; 105(8): 1871-81, 2013 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-24138863

RESUMO

Generation of force and movement by actomyosin cross-bridges is the molecular basis of muscle contraction, but generally accepted ideas about cross-bridge properties have recently been questioned. Of the utmost significance, evidence for nonlinear cross-bridge elasticity has been presented. We here investigate how this and other newly discovered or postulated phenomena would modify cross-bridge operation, with focus on post-power-stroke events. First, as an experimental basis, we present evidence for a hyperbolic [MgATP]-velocity relationship of heavy-meromyosin-propelled actin filaments in the in vitro motility assay using fast rabbit skeletal muscle myosin (28-29°C). As the hyperbolic [MgATP]-velocity relationship was not consistent with interhead cooperativity, we developed a cross-bridge model with independent myosin heads and strain-dependent interstate transition rates. The model, implemented with inclusion of MgATP-independent detachment from the rigor state, as suggested by previous single-molecule mechanics experiments, accounts well for the [MgATP]-velocity relationship if nonlinear cross-bridge elasticity is assumed, but not if linear cross-bridge elasticity is assumed. In addition, a better fit is obtained with load-independent than with load-dependent MgATP-induced detachment rate. We discuss our results in relation to previous data showing a nonhyperbolic [MgATP]-velocity relationship when actin filaments are propelled by myosin subfragment 1 or full-length myosin. We also consider the implications of our results for characterization of the cross-bridge elasticity in the filament lattice of muscle.


Assuntos
Actomiosina/metabolismo , Elasticidade , Músculo Esquelético/metabolismo , Dinâmica não Linear , Citoesqueleto de Actina/efeitos dos fármacos , Citoesqueleto de Actina/metabolismo , Trifosfato de Adenosina/farmacologia , Animais , Fenômenos Biomecânicos/efeitos dos fármacos , Elasticidade/efeitos dos fármacos , Modelos Biológicos , Músculo Esquelético/efeitos dos fármacos , Subfragmentos de Miosina/metabolismo , Coelhos
6.
Amino Acids ; 43(4): 1471-83, 2012 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22286872

RESUMO

Salt-bridge interactions between acidic and basic amino acids contribute to the structural stability of proteins and to protein-protein interactions. A conserved salt-bridge is a canonical feature of the α-defensin antimicrobial peptide family, but the role of this common structural element has not been fully elucidated. We have investigated mouse Paneth cell α-defensincryptdin-4 (Crp4) and peptide variants with mutations at Arg7 or Glu15 residue positions to disrupt the salt-bridge and assess the consequences on Crp4 structure, function, and stability. NMR analyses showed that both (R7G)-Crp4 and (E15G)-Crp4 adopt native-like structures, evidence of fold plasticity that allows peptides to reshuffle side chains and stabilize the structure in the absence of the salt-bridge. In contrast, introduction of a large hydrophobic side chain at position 15, as in (E15L)-Crp4 cannot be accommodated in the context of the Crp4 primary structure. Regardless of which side of the salt-bridge was mutated, salt-bridge variants retained bactericidal peptide activity with differential microbicidal effects against certain bacterial cell targets, confirming that the salt-bridge does not determine bactericidal activity per se. The increased structural flexibility induced by salt-bridge disruption enhanced peptide sensitivity to proteolysis. Although sensitivity to proteolysis by MMP7 was unaffected by most Arg(7) and Glu(150 substitutions, every salt-bridge variant was degraded extensively by trypsin. Moreover, the salt-bridge facilitates adoption of the characteristic α-defensin fold as shown by the impaired in vitro refolding of (E15D)-proCrp4, the most conservative salt-bridge disrupting replacement. In Crp4, therefore, the canonical α-defensin salt-bridge facilitates adoption of the characteristic α-defensin fold, which decreases structural flexibility and confers resistance todegradation by proteinases.


Assuntos
Anti-Infecciosos/química , alfa-Defensinas/química , Sequência de Aminoácidos , Animais , Anti-Infecciosos/farmacologia , Arginina/química , Arginina/genética , Ácido Glutâmico/química , Ácido Glutâmico/genética , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Negativas/crescimento & desenvolvimento , Bactérias Gram-Positivas/efeitos dos fármacos , Bactérias Gram-Positivas/crescimento & desenvolvimento , Interações Hidrofóbicas e Hidrofílicas , Espectroscopia de Ressonância Magnética , Metaloproteinase 7 da Matriz/química , Camundongos , Viabilidade Microbiana/efeitos dos fármacos , Dados de Sequência Molecular , Mutação , Celulas de Paneth/fisiologia , Estabilidade Proteica , Estrutura Secundária de Proteína , Proteólise , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/farmacologia , Sais , Tripsina/química , alfa-Defensinas/genética , alfa-Defensinas/farmacologia
7.
Water Res ; 218: 118477, 2022 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-35487159

RESUMO

A large pilot-scale granular activated carbon (GAC) filter was operated downstream in a full-scale wastewater treatment plant to remove organic micropollutants. To describe the spatial and temporal developments of micropollutant adsorption profiles in the GAC filter, micropollutants were extracted from GAC media taken at various filter depths and number of treated bed volumes. At a low number of treated bed volumes (2600 BVs), most micropollutants were adsorbed in the top layers of the filter. At increasing number of treated bed volumes (7300-15,500 BVs), the adsorption front for micropollutants progressed through the filter bed at varying rates, with sulfamethoxazole, fluconazole, and PFOS reaching the bottom layer before carbamazepine and other well-adsorbing micropollutants, such as propranolol and citalopram. Higher amounts of adsorbed micropollutants in the bottom layer of the filter bed resulted in decreased removal efficiencies in the treated wastewater. Mass estimations indicated biodegradation for certain micropollutants, such as naproxen, diclofenac, and sulfamethoxazole. A temporary increase in the concentration of the insecticide imidacloprid could be detected in the filter indicating that extraction of adsorbed micropollutants could provide an opportunity for backtracking of loading patterns.


Assuntos
Poluentes Químicos da Água , Purificação da Água , Adsorção , Carvão Vegetal , Sulfametoxazol , Eliminação de Resíduos Líquidos/métodos , Águas Residuárias , Poluentes Químicos da Água/análise , Purificação da Água/métodos
8.
Cytoskeleton (Hoboken) ; 70(11): 718-28, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-24039103

RESUMO

Actin filaments are central components of the cytoskeleton and the contractile machinery of muscle. The filaments are known to exist in a range of conformational states presumably with different flexural rigidity and thereby different persistence lengths. Our results analyze the approaches proposed previously to measure the persistence length from the statistics of the winding paths of actin filaments that are propelled by surface-adsorbed myosin motor fragments in the in vitro motility assay. Our results suggest that the persistence length of heavy meromyosin propelled actin filaments can be estimated with high accuracy and reproducibility using this approach provided that: (1) the in vitro motility assay experiments are designed to prevent bias in filament sliding directions, (2) at least 200 independent filament paths are studied, (3) the ratio between the sliding distance between measurements and the camera pixel-size is between 4 and 12, (4) the sliding distances between measurements is less than 50% of the expected persistence length, and (5) an appropriate cut-off value is chosen to exclude abrupt large angular changes in sliding direction that are complications, e.g., due to the presence of rigor heads. If the above precautions are taken the described method should be a useful routine part of in vitro motility assays thus expanding the amount of information to be gained from these.


Assuntos
Citoesqueleto de Actina/química , Membrana Celular/metabolismo , Miosinas/metabolismo , Citoesqueleto de Actina/metabolismo , Adsorção , Simulação por Computador , Método de Monte Carlo , Reprodutibilidade dos Testes
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