RESUMO
Skin is the largest human organ with easily noticeable biophysical manifestations of aging. As human tissues age, there is chronological accumulation of biophysical changes due to internal and environmental factors. Skin aging leads to decreased elasticity and the loss of dermal matrix integrity via degradation. The mechanical properties of the dermal matrix are maintained by fibroblasts, which undergo replicative aging and may reach senescence. While the secretory phenotype of senescent fibroblasts is well studied, little is known about changes in the fibroblasts biophysical phenotype. Therefore, we compare biophysical properties of young versus proliferatively aged primary fibroblasts via fluorescence and traction force microscopy, single-cell atomic force spectroscopy, microfluidics, and microrheology of the cytoskeleton. Results show senescent fibroblasts have decreased cytoskeletal tension and myosin II regulatory light chain phosphorylation, in addition to significant loss of traction force. The alteration of cellular forces is harmful to extracellular matrix homeostasis, while decreased cytoskeletal tension can amplify epigenetic changes involved in senescence. Further exploration and detection of these mechanical phenomena provide possibilities for previously unexplored pharmaceutical targets against aging.
Assuntos
Senescência Celular , Pele , Humanos , Idoso , Senescência Celular/genética , Células Cultivadas , Envelhecimento , Fibroblastos/metabolismoRESUMO
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: ⢠Fast and easy analysis. ⢠Universal applicability shown for a series of real successful projects.
Assuntos
Bioensaio , Oligonucleotídeos , Controle de Qualidade , TemperaturaRESUMO
BACKGROUND: Ventricular dilation is known as a pivotal predictor in recent-onset cardiomyopathy (ROCM), but its pathophysiology is not fully understood. In the present study we investigated whether single-cell stiffness of right and left ventricular-derived fibroblasts has an effect on cardiac phenotype in patients with ROCM. METHODS AND RESULTS: Patients with endomyocardial biopsy-proven ROCM were included (n=10). Primary cardiac fibroblasts (CFBs) were cultured from left and right ventricular endomyocardial biopsies and their single-cell stiffness was analyzed by quantification of Young's modulus using colloidal probe atomic force microscopy. Cardiac fibrosis was analyzed by Masson's trichrome staining. CFBs from the left ventricle showed significantly decreased stiffness when compared with CFBs from the right ventricle, indexed by decreased stiffness (Young's modulus 3,374±389 vs. 4,837±690 Pa; P<0.05). Young's modulus of CFBs derived from the left ventricle correlated negatively with the left ventricular end-diastolic dimension derived from 2-dimensional echocardiography (R(2)=0.77; P<0.01). Neither left nor right ventricular fibrosis correlated with the respective ventricular dimensions. CONCLUSIONS: Our data suggest that a decrease in single-cell stiffness of left ventricular fibroblasts could trigger left ventricular dilation in patients with ROCM. This implies a new potential mechanism for the ventricular dilation with this disease.
Assuntos
Cardiomiopatia Dilatada , Módulo de Elasticidade , Fibroblastos , Ventrículos do Coração , Adulto , Idoso , Cardiomiopatia Dilatada/metabolismo , Cardiomiopatia Dilatada/patologia , Cardiomiopatia Dilatada/fisiopatologia , Feminino , Fibroblastos/metabolismo , Fibroblastos/ultraestrutura , Ventrículos do Coração/metabolismo , Ventrículos do Coração/patologia , Ventrículos do Coração/fisiopatologia , Humanos , Masculino , Microscopia de Força Atômica , Pessoa de Meia-IdadeRESUMO
Upon aging, the function of the intestinal epithelium declines with a concomitant increase in aging-related diseases. ISCs play an important role in this process. It is known that ISC clonal dynamics follow a neutral drift model. However, it is not clear whether the drift model is still valid in aged ISCs. Tracking of clonal dynamics by clonal tracing revealed that aged crypts drift into monoclonality substantially faster than young ones. However, ISC tracing experiments, in vivo and ex vivo, implied a similar clonal expansion ability of both young and aged ISCs. Single-cell RNA sequencing for 1,920 high Lgr5 ISCs from young and aged mice revealed increased heterogeneity among subgroups of aged ISCs. Genes associated with cell adhesion were down-regulated in aged ISCs. ISCs of aged mice indeed show weaker adhesion to the matrix. Simulations applying a single cell-based model of the small intestinal crypt demonstrated an accelerated clonal drift at reduced adhesion strength, implying a central role for reduced adhesion for affecting clonal dynamics upon aging.
Assuntos
Intestinos , Células-Tronco , Animais , Células Cultivadas , Íleo , Mucosa Intestinal/metabolismo , Camundongos , Células-Tronco/metabolismoRESUMO
Throughout life, the body is subjected to various mechanical forces on the organ, tissue, and cellular level. Mechanical stimuli are essential for organ development and function. One organ whose function depends on the tightly connected interplay between mechanical cell properties, biochemical signaling, and external forces is the lung. However, altered mechanical properties or excessive mechanical forces can also drive the onset and progression of severe pulmonary diseases. Characterizing the mechanical properties and forces that affect cell and tissue function is therefore necessary for understanding physiological and pathophysiological mechanisms. In recent years, multiple methods have been developed for cellular force measurements at multiple length scales, from subcellular forces to measuring the collective behavior of heterogeneous cellular networks. In this short review, we give a brief overview of the mechanical forces at play on the cellular level in the lung. We then focus on the technological aspects of measuring cellular forces at many length scales. We describe tools with a subcellular resolution and elaborate measurement techniques for collective multicellular units. Many of the technologies described are by no means restricted to lung research and have already been applied successfully to cells from various other tissues. However, integrating the knowledge gained from these multi-scale measurements in a unifying framework is still a major future challenge.
RESUMO
Formation of transient protein complexes is an important process in cells. Details of the association process as well as the energy landscapes of association are not well understood. In particular, the nature, height and position of the energy barriers during complexation are debated. Computational studies are well suited for atomistically investigating protein association processes. The Barnase-Barstar complex constitutes a well-studied target for computational studies as a small system with fast association rates. Here, we performed constraint biased Molecular Dynamics simulations along the reaction coordinate reaching from the diffusion regime to the bound complex. We simulated the wild-type and different mutants at different salt concentrations. A structural analysis of our simulation trajectories revealed not a single, but two distinct association patterns dominated by an interplay between two charged contact points near the binding site. Electrostatics and/or mutations influence the relative population of these patterns. Further, we computed the energy landscape of association as PMF (Potential of Mean Force) profiles within a reasonable agreement to experiment. We find a single energy barrier at a distance of ~0.3 nm, which corresponds to the final desolvation transition. Electrostatics has a profound influence on the height of this energy barrier, but not on its position.
Assuntos
Proteínas de Bactérias/química , Simulação de Dinâmica Molecular , Ribonucleases/química , Proteínas de Bactérias/genética , Sítios de Ligação , Cinética , Mutação , Conformação Proteica , Ribonucleases/genética , Eletricidade EstáticaRESUMO
Protein-surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnology to medicine. A recent workshop highlighted the current achievements and the main challenges in the field.
Assuntos
Simulação por Computador , Proteínas , Animais , Íons/química , Modelos Moleculares , Peptídeos/química , Peptídeos/metabolismo , Conformação Proteica , Proteínas/química , Proteínas/metabolismo , Propriedades de Superfície , Água/químicaRESUMO
The pathogenic yeast Candida auris has received increasing attention due to its ability to cause fatal infections, its resistance toward important fungicides, and its ability to persist on surfaces including medical devices in hospitals. To brace health care systems for this considerable risk, alternative therapeutic approaches such as antifungal peptides are urgently needed. In clinical wound care, a significant focus has been directed toward novel surgical (wound) dressings as first defense lines against C. auris. Inspired by Cerberus the Greek mythological "hound of Hades" that prevents the living from entering and the dead from leaving hell, the preparation of a gatekeeper hybrid hydrogel is reported featuring lectin-mediated high-affinity immobilization of C. auris cells from a collagen gel as a model substratum in combination with a release of an antifungal peptide drug to kill the trapped cells. The vision is an efficient and safe two-layer medical composite hydrogel for the treatment of severe wound infections that typically occur in hospitals. Providing this new armament to the repertoire of possibilities for wound care in critical (intensive care) units may open new routes to shield and defend patients from infections and clinical facilities from spreading and invasion of C. auris and probably other fungal pathogens.
Assuntos
Antifúngicos/farmacologia , Candida/efeitos dos fármacos , Farmacorresistência Fúngica Múltipla/efeitos dos fármacos , Hidrogéis/farmacologia , Peptídeos/farmacologia , Animais , Antifúngicos/síntese química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bandagens , Candida/crescimento & desenvolvimento , Candida/patogenicidade , Colágeno/química , Expressão Gênica , Humanos , Hidrogéis/química , Lectinas/genética , Lectinas/metabolismo , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Metionina/química , Testes de Sensibilidade Microbiana , Compostos Organofosforados/química , Peptídeos/síntese química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Soroalbumina Bovina/química , Pele/efeitos dos fármacos , Suínos , Compostos de Tritil/químicaRESUMO
The beta subunit of Na,K-ATPase is required for stabilization and maturation of the catalytic alpha subunits and is also involved in cell adhesion and establishing epithelial cell polarity. However, the mechanism of cell adhesion effects and protein partners of beta are unknown. We have applied fold recognition methods to predict that a C-terminal domain of the beta subunits of Na,K-ATPase and H,K-ATPase has an immunoglobulin-like fold, which resembles cell adhesion molecules. Comparison of the predicted C-terminal domain with a recently published structure of shark rectal gland Na,K-ATPase at 2.4 A in which alpha, beta, and FXYD subunits were resolved confirms that the beta subunit ectodomain contains an immunoglobulin-like structure. Expression in Escherichia coli of a sequence corresponding to the C-terminal domain, followed by its purification, refolding, and circular dichroism analysis, shows that the domain is independently stable with prominent beta sheet secondary structure, as predicted. Proteolytic digestion of the purified detergent-soluble recombinant Na,K-ATPase (alpha1beta1) is also indicative of a stable C-terminal domain of beta in the native complex. The major conclusion of this work is consistent with prior evidence for a role of the beta subunit in cell-cell adhesion, and it attributes that function largely to the C-terminal lobe of the beta ectodomain. In the light of these findings, we discuss its role in cell adhesion and recognition of the beta subunits of Na,K-ATPase, including potential protein partners.
Assuntos
Moléculas de Adesão Celular/química , ATPase Trocadora de Hidrogênio-Potássio/química , Fragmentos de Peptídeos/química , Subunidades Proteicas/química , ATPase Trocadora de Sódio-Potássio/química , Homologia Estrutural de Proteína , Sequência de Aminoácidos , Animais , Humanos , Imunoglobulinas/química , Isoenzimas/química , Modelos Moleculares , Dados de Sequência Molecular , Valor Preditivo dos Testes , Dobramento de Proteína , Estrutura Terciária de Proteína , Alinhamento de Sequência , TubarõesRESUMO
Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids. Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded. We discovered that upon refolding certain helices are pulled into the membrane against a sizable external force of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
Assuntos
Bacteriorodopsinas/química , Membrana Celular/química , Halobacterium/química , Dobramento de Proteína , Renaturação Proteica , Estrutura Terciária de Proteína , Bacteriorodopsinas/metabolismo , Microscopia de Força Atômica , Estrutura Secundária de ProteínaRESUMO
Adhesion of monocytes to micro-injuries on arterial walls is an important early step in the occurrence and development of degenerative atherosclerotic lesions. At these injuries, collagen is exposed to the blood stream. We are interested whether age influences monocyte adhesion to collagen under flow, and hence influences the susceptibility to arteriosclerotic lesions. Therefore, we studied adhesion and rolling of human peripheral blood monocytes from old and young individuals on collagen type I coated surface under shear flow. We find that firm adhesion of monocytes to collagen type I is elevated in old individuals. Pre-stimulation by lipopolysaccharide increases the firm adhesion of monocytes homogeneously in older individuals, but heterogeneously in young individuals. Blocking integrin αx showed that adhesion of monocytes to collagen type I is specific to the main collagen binding integrin αxß2. Surprisingly, we find no significant age-dependent difference in gene expression of integrin αx or integrin ß2. However, if all integrins are activated from the outside, no differences exist between the age groups. Altered integrin activation therefore causes the increased adhesion. Our results show that the basal increase in integrin activation in monocytes from old individuals increases monocyte adhesion to collagen and therefore the risk for arteriosclerotic plaques.
Assuntos
Envelhecimento/metabolismo , Aterosclerose/metabolismo , Colágeno Tipo I/metabolismo , Integrina alfaXbeta2/metabolismo , Migração e Rolagem de Leucócitos , Monócitos/metabolismo , Adulto , Idoso , Envelhecimento/patologia , Aterosclerose/patologia , Adesão Celular , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Monócitos/patologiaRESUMO
De novo design and redesign of proteins and protein complexes have made promising progress in recent years. Here, we give an overview of how to use available computer-based tools to design proteins to bind faster and tighter to their protein-complex partner by electrostatic optimization between the two proteins. Electrostatic optimization is possible because of the simple relation between the Debye-Huckel energy of interaction between a pair of proteins and their rate of association. This can be used for rapid, structure-based calculations of the electrostatic attraction between the two proteins in the complex. Using these principles, we developed two computer programs that predict the change in k(on), and as such the affinity, on introducing charged mutations. The two programs have a web interface that is available at
Assuntos
Modelos Moleculares , Complexos Multiproteicos/química , Engenharia de Proteínas , Proteínas/química , Proteômica , Software , Sítios de Ligação/genética , Bases de Dados de Proteínas , Internet , Complexos Multiproteicos/genética , Mutação , Valor Preditivo dos Testes , Ligação Proteica/genética , Conformação Proteica , Engenharia de Proteínas/métodos , Mapeamento de Interação de Proteínas , Estrutura Quaternária de Proteína/genética , Proteínas/genética , Proteômica/métodos , Eletricidade EstáticaRESUMO
Integrins are composed of noncovalently bound dimers of an alpha- and a beta-subunit. They play an important role in cell-matrix adhesion and signal transduction through the cell membrane. Signal transduction can be initiated by the binding of intracellular proteins to the integrin. Binding leads to a major conformational change. The change is passed on to the extracellular domain through the membrane. The affinity of the extracellular domain to certain ligands increases; thus at least two states exist, a low-affinity and a high-affinity state. The conformations and conformational changes of the transmembrane (TM) domain are the focus of our interest. We show by a global search of helix-helix interactions that the TM section of the family of integrins are capable of adopting a structure similar to the structure of the homodimeric TM protein Glycophorin A. For the alpha(IIb)beta(3) integrin, this structural motif represents the high-affinity state. A second conformation of the TM domain of alpha(IIb)beta(3) is identified as the low-affinity state by known mutational and nuclear magnetic resonance (NMR) studies. A transition between these two states was determined by molecular dynamics (MD) calculations. On the basis of these calculations, we propose a three-state mechanism.
Assuntos
Integrina alfa2/metabolismo , Integrina beta3/metabolismo , Transdução de Sinais , Sequência de Aminoácidos , Animais , Humanos , Glicoproteínas de Membrana/metabolismo , Dados de Sequência Molecular , Conformação Proteica , Estrutura Terciária de Proteína , Alinhamento de SequênciaRESUMO
The structures of membrane transporters are still mostly unsolved. Only recently, the first two high-resolution structures of transporters of the major facilitator superfamily (MFS) were published. Despite the low sequence similarity of the two proteins involved, lactose permease and glycerol-3-phosphate transporter, the reported structures are highly similar. This leads to the hypothesis that all members of the MFS share a similar structure, regardless of their low sequence identity. To test this hypothesis, we generated models of two other members of the MFS, the Tn10-encoded metal-tetracycline/H(+) antiporter (TetAB) and the rat vesicular monoamine transporter (rVMAT2). The models are based on the two MFS structures and on experimental data. The models for both proteins are in good agreement with the data available and support the notion of a shared fold for all MFS proteins.
Assuntos
Antiporters/química , Proteínas de Bactérias/química , Simulação por Computador , Glicoproteínas de Membrana/química , Proteínas de Membrana Transportadoras/química , Homologia Estrutural de Proteína , Animais , Ratos , Proteínas Vesiculares de Transporte de Aminas Biogênicas , Proteínas Vesiculares de Transporte de MonoaminaRESUMO
Integrins are pivotal proteins in cell-cell adhesion, signaling and apoptosis. These properties render them attractive targets for drugs, especially those involved in cancer treatment. Recently, the structures of the extracellular domains of one of the integrin subtypes was solved with X-ray crystallography in the free form as well as bound to a ligand. These structures in combination with NMR spectroscopic data, electron microscopy images, and molecular modeling provide deeper insight into the mechanism of integrin-mediated signal transduction. The structures make structure-based rational drug design possible and are certainly hallmarks in integrin research.
Assuntos
Desenho de Fármacos , Integrinas/química , Transdução de Sinais , Humanos , Integrinas/uso terapêutico , Ligantes , Modelos Moleculares , Estrutura Molecular , Ligação Proteica , Estrutura Terciária de ProteínaRESUMO
Starting from the first crystal structure of the extracellular segment of the alpha(v)beta(3) integrin receptor with a cyclic RGD ligand bound to the active site, structural models for the interactions of known ligands with the alpha(v)beta(3) integrin receptor were generated by automated computational docking. The obtained complexes were evaluated for their consistency with structure-activity relationships and site-directed mutagenesis data. A comparison between the calculated interaction free energies and the experimental biological activities was also made. All the possible interactions of the investigated compounds at the active site and the probable ligand binding conformations provide an improved basis for structure-based rational ligand design. Additionally, our docking results allow a further validation and refinement of the pharmacophore model previously postulated by us.
Assuntos
Integrina alfaVbeta3/química , Algoritmos , Benzodiazepinas/síntese química , Benzodiazepinas/farmacologia , Cristalização , Cristalografia por Raios X , Desenho de Fármacos , Ligação de Hidrogênio , Integrina alfaVbeta3/efeitos dos fármacos , Integrina alfaVbeta3/genética , Ligantes , Modelos Moleculares , Conformação Molecular , Método de Monte Carlo , Mutagênese Sítio-Dirigida , Oligopeptídeos , Conformação Proteica , Estereoisomerismo , Relação Estrutura-AtividadeRESUMO
The recently reported crystal structures of the extracellular domains of the alphavbeta3 integrin in its unligated state and in complex with the peptide cyclo(-RGDf[NMe]V-) have dramatically increased our understanding of ligand binding to integrins. Nonetheless, ligand selectivity toward different integrin subtypes is still a challenging problem complicated by the fact that 3D structures of most of the integrin subtypes remain unknown. In this study, a three-dimensional model for the human alphavbeta5 integrin was obtained using homology modeling based on the crystal coordinates of alphavbeta3 in its bound conformation as template. The modeled receptor was refined using energy minimization and molecular dynamics simulations in explicit solvent. The refined alphavbeta5 model was used to explore the interactions between this integrin and alphavbeta3/alphavbeta5 dual and alphavbeta3-selective ligands in the attempt to provide a preliminary rationalization, at the molecular level, of ligand selectivity toward the two alphav integrins. It was found that, in the RGD binding site of the alphavbeta5 receptor, a partial "roof" composed mainly of the SDL residues Tyr179 and Lys180 is present and hampers the binding of compounds containing bulky substituents in the proximity of the carboxylate group. This study provides a testable hypothesis for alphav integrins subtype ligand binding selectivity, in line with both mutagenesis data and SARs studies.
Assuntos
Integrinas/química , Receptores de Vitronectina/química , Sequência de Aminoácidos , Humanos , Integrina alfaVbeta3/química , Ligantes , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Molecular , Ligação Proteica , Homologia de Sequência de AminoácidosRESUMO
How different integrins that bind to the same type of extracellular matrix protein mediate specific functions is unclear. We report the functional analysis of ß1- and αv-class integrins expressed in pan-integrin-null fibroblasts seeded on fibronectin. Reconstitution with ß1-class integrins promotes myosin-II-independent formation of small peripheral adhesions and cell protrusions, whereas expression of αv-class integrins induces the formation of large focal adhesions. Co-expression of both integrin classes leads to full myosin activation and traction-force development on stiff fibronectin-coated substrates, with αv-class integrins accumulating in adhesion areas exposed to high traction forces. Quantitative proteomics linked αv-class integrins to a GEF-H1-RhoA pathway coupled to the formin mDia1 but not myosin II, and α5ß1 integrins to a RhoA-Rock-myosin II pathway. Our study assigns specific functions to distinct fibronectin-binding integrins, demonstrating that α5ß1integrins accomplish force generation, whereas αv-class integrins mediate the structural adaptations to forces, which cooperatively enable cells to sense the rigidity of fibronectin-based microenvironments.
Assuntos
Microambiente Celular , Fibronectinas/metabolismo , Integrina alfaV/metabolismo , Integrina beta1/metabolismo , Miosina Tipo II/metabolismo , Animais , Proteínas de Transporte/metabolismo , Adesão Celular , Linhagem Celular , Movimento Celular , Matriz Extracelular/metabolismo , Proteínas da Matriz Extracelular/metabolismo , Fibroblastos , Adesões Focais/metabolismo , Forminas , Fatores de Troca do Nucleotídeo Guanina/genética , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Integrina alfa5beta1/metabolismo , Masculino , Camundongos , Camundongos Transgênicos , Ligação Proteica , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Proto-Oncogênicas/genética , Proteínas Proto-Oncogênicas/metabolismo , Interferência de RNA , RNA Interferente Pequeno , Fatores de Troca de Nucleotídeo Guanina Rho , Quinases Associadas a rho/metabolismo , Proteína rhoA de Ligação ao GTP/metabolismoRESUMO
Great progress has been made in the design and synthesis of molecular motors and rotors. Loosely inspired by biomolecular machines such as kinesin and the FoF1 ATPsynthase, these molecules are hoped to provide elements for construction of more elaborate structures that can carry out tasks at the nanoscale corresponding to the tasks accomplished by elementary machines in the macroscopic world. Most of the molecular motors synthesized to date suffer from the drawback that they operate relatively slowly (less than kHz). Here we show by molecular dynamics studies of a diethyl sulfide rotor on a gold(111) surface that a high-frequency oscillating electric field normal to the surface can drive directed rotation at GHz frequencies. The maximum directed rotation rate is 10(10) rotations per second, significantly faster than the rotation of previously reported directional molecular rotors. Understanding the fundamental basis of directed motion of surface rotors is essential for the further development of efficient externally driven artificial rotors. Our results represent a step toward the design of a surface-bound molecular rotary motor with a tunable rotation frequency and direction.
Assuntos
Modelos Químicos , Sulfetos/química , Simulação por Computador , Transferência de Energia/efeitos da radiação , Doses de Radiação , Radiação TerahertzRESUMO
In order to study protein-inorganic surface association processes, we have developed a physics-based energy model, the ProMetCS model, which describes protein-surface interactions at the atomistic level while treating the solvent as a continuum. Here, we present an approach to modeling the interaction of a protein with an atomically flat Au(111) surface in an aqueous solvent. Protein-gold interactions are modeled as the sum of van der Waals, weak chemisorption, and electrostatic interactions, as well as the change in free energy due to partial desolvation of the protein and the metal surface upon association. This desolvation energy includes the effects of water-protein, water-surface, and water-water interactions and has been parametrized using molecular dynamics (MD) simulations of water molecules and a test atom at a gold-water interface. The proposed procedure for computing the energy terms is mostly grid-based and is therefore efficient for application to long-time simulations of protein binding processes. The approach was tested for capped amino acid residues whose potentials of mean force for binding to a gold surface were computed and compared with those obtained previously in MD simulations with water treated explicitly. Calculations show good quantitative agreement with the results from MD simulations for all but one amino acid (Trp), as well as correspondence with available experimental data on the adhesion properties of amino acids.