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1.
    
Carbon nanomaterials are receiving an increasingly large interest in a variety of fields, including also nanomedicine. In this area, much attention is devoted to investigating and modeling the behavior of these nanomaterials when they interact with biological fluids and with biological macromolecules, in particular proteins and oligopeptides. The interaction with these molecules is in fact crucial to understand and predict the efficacy of nanomaterials as drug carriers or therapeutic agents as well as their potential toxicity when they occupy the active site of a protein or severely affect the secondary and tertiary structure, or even the local dynamics, thus inhibiting their biological function. In this review, therefore, we describe the most recent work carried out in the last few years to model the interaction between carbon nanomaterials, either pristine or functionalized, and proteins or oligopeptides using classical atomistic methods, mainly molecular dynamics simulations. The attention is focused on 0-dimensional fullerenes, mainly C60, on 1-dimensional carbon nanotubes, mostly the single-walled armchair and some chiral ones, and on 2-dimensional graphene and graphyne, the latter containing also sp hybridized atoms in addition to the sp2 ones common to the other carbon nanomaterials.  相似文献   

2.
Classical molecular dynamics (MD) and non-equilibrium steered molecular dynamics (SMD) simulations were performed on the molecular structure of the potassium channel KcsA using the GROMOS 87 force fields. Our simulations focused on mechanistic and dynamic properties of the permeation of potassium ions through the selectivity filter of the channel. According to the SMD simulations a concerted movement of ions inside the selectivity filter from the cavity to extracellular side depends on the conformation of the peptide linkage between Val76 and Gly77 residues in one subunit of the channel. In SMD simulations, if the carbonyl oxygen of Val76 is positioned toward the ion bound at the S3 site (gate-opened conformation) the net flux of ions through the filter is observed. When the carbonyl oxygen leaped out from the filter (gate-closed conformation), ions were blocked at the S3 site and no flux occurred. A reorientation of the Thr75-Val76 linkage indicated by the CHARMM-based MD simulations performed Berneche and Roux [(2005) Structure 13:591–600; (2000) Biophys J 78:2900–2917] as a concomitant process of the Val76-Gly77 conformational interconversion was not observed in our GROMOS-based MD simulations.  相似文献   

3.
    
Protein adsorption, which shows wide prospects in many practical applications such as biosensors, biofuel cells, and biomaterials, has long been identified as a very complex problem in interface science. Here, we present a review on the multiscale modeling and simulation methods of protein adsorption on surfaces with different properties. First, various simulation algorithms (replica exchange, metadynamics, TIGER2A, and PSOVina) and protein models (colloidal, coarse-grained, and all-atom models) are introduced. Then, recent molecular simulation progresses about protein adsorption on different material surfaces (such as charged, hydrophobic, hydrophilic, and responsive surfaces) are retrospected. It has been demonstrated that the adsorption orientation of proteins on charged surfaces and hydrophobic surfaces can be controlled by the electrical dipole and the hydrophobic dipole of proteins, respectively. Superhydrophilic zwitterionic surfaces can resist protein adsorption because of the strong hydration. Under the stimuli of external conditions, the surface properties of materials can be modulated, and thus, the adsorption/desorption of proteins on responsive surfaces can be controlled. Finally, the future directions of molecular simulation study of protein adsorption are discussed.  相似文献   

4.
The adsorption of proteins at surfaces and interfaces is important in a wide range of industries. Understanding and controlling the conformation of adsorbed proteins at surfaces is critical to stability and function in many technological applications including foods and biomedical testing kits or sensors. Studying adsorbed protein conformation is difficult experimentally and so over the past few decades researchers have turned to computer simulation methods to give information at the atomic level on this important area. In this review we summarize some of the significant simulation work over the past four years at both fluid (liquid–liquid and gas–liquid interfaces) and solid–liquid interfaces. Of particular significance is the work on surfactant proteins such as fungal hydrophobins, ranspumin-2 from the túngara frog and the bacteria protein BslA. These have evolved unique structures impart very high surface-active properties to the molecules. A highlight is the elucidation of the clam-shell unhinging mechanism of ranspumin-2 adsorption to the gas–liquid interface that is responsible for its adsorption to and stabilization of the air bubbles in túngara frog foam nests.  相似文献   

5.
    
Protein internal dynamics is essential for its function.Exploring the internal dynamics of protein molecules as well as its connection to protein structure and function is a central topic in biophysics.However,the atomic motions in protein molecules exhibit a great degree of complexities.These complexities arise from the complex chemical composition and superposition of different types of atomic motions on the similar time scales,and render it challenging to explicitly understand the microscopic mechanism governing protein motions,functions,and their connections.Here,we demonstrate that,by using neutron scattering,molecular dynamics simulation,and deuteration technique,one can address this challenge to a large extent.  相似文献   

6.
We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations and is limited in accuracy only by the numerical methods for solving small systems of linear equations. As a result of the non-iterative and exact (within numerical accuracy) nature of the procedure, there is no drift in the constrained geometry, and the method is therefore readily applied to molecular dynamics simulations of, for example, rigid linear molecules or materials of non-spherical grains. We illustrate the approach through implementation in the commonly used second-order velocity-explicit Verlet method. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 911-916, 2005  相似文献   

7.
Molecular dynamics simulations have been performed on oligo(ethylene oxide)s of various molecular weights doped with the lithium bis(trifluoromethanesulfonyl)imide salt (LiTFSI) in order to explore the mechanism of Li+ transport in materials covering the range from liquid electrolytes to prototypes for high molecular weight poly(ethylene oxide)-based polymer electrolytes. Good agreement between MD simulations and experiments is observed for the conductivity of electrolytes as a function of molecular weight. Unlike Li+ transport in liquid ethylene carbonate (EC) that comes from approximately equal contributions of vehicular Li+ motion (motion together with solvent) and Li+ diffusion by solvent exchange, Li+ transport in oligoethers was found to occur predominantly by vehicular motion. The slow solvent exchange of Li+ in oligo(ethylene oxide)s highlights why high molecular weight amorphous polymer electrolytes with oligo(ethylene oxide)s solvating groups suffer from poor Li+ transport. Ion complexation and correlation of cation and anion motion is examined for oligoethers and compared with that in EC.  相似文献   

8.
    
Two bead-spring models of flexible chains for generic coarse graining of entangled polymer melts, the excluded volume Kremer–Grest (KG) model and the modified segmental repulsive potential (mSRP) combined with a weakly repulsive potential, are compared. For chains containing an equivalent number of entanglements, we compare the chain characteristics of the KG and mSRP polymer models by determining the ratios of the entanglement lengths , the required total number of particles to capture comparable entanglement phenomena , and the time scaling ratios τmSRP/τKG. Our findings show that systems using the mSRP polymer model require half the number of particles and relax four times faster compared to the KG polymer model. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012  相似文献   

9.
    
The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.  相似文献   

10.
Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglutamine chains 16 residues long at a concentration of 5 mM spontaneously formed large beta sheets which curved to form tube-like annular structures that resemble beta barrels. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms depending on the residue being modeled. Our results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglutamine forms water filled nanotubes.  相似文献   

11.
    
Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional (3D) Langevin dynamics simulations, we investigate adsorption behaviors of multivalent polymer chains to a surface with receptors. Multivalent polymer chains display superselective adsorption. Furthermore, the range of density of surface receptors at which a multivalent polymer chain displays a superselective behavior, narrows down for chains with higher density of ligands. Meanwhile, the optimal density of surface receptors where the highest superselectivity is achieved, decreases with increasing the density of ligands. Then, the conformational properties of bound multivalent chains are studied systematically. Interestingly, we find that the equilibrium radius of gyration Rg and its horizontal component have a maximum as a function of the density of surface receptors. The scaling exponents of Rg with the length of chain suggest that with increasing the density of surface receptors., the conformations of a bound multivalent polymer chain first fall in between those of a two-dimensional (2D) and a 3D chain, while it is slightly collapsed subsequently.  相似文献   

12.
    
Directed evolution involves iterative rounds of genetic diversification followed by selection of variants with improved enzyme properties. A common trend in these studies is the introduction of multiple scattered mutations remote from the active site. Rationalizing how distal mutations influence the conformational states or ensemble of conformations formed by enzymes, and its relation to enzymatic catalysis is highly appealing for the improvement of current rational enzyme design strategies. Directed evolution was applied to convert d-sialic acid aldolase into an efficient l-3-deoxy-manno-2-octulosonic acid (l-KDO) aldolase. In this study, we computationally evaluate the conformational dynamics of both enzymes to shed light on the specificity of the evolved variant. We further demonstrate the role of distal mutations on the modulation of enzyme conformational dynamics and its relation to substrate accessibility and selectivity. Mutations markedly altered the active site shape and substrate access tunnels in the evolved l-KDO aldolase, thus affecting the enzyme specificity.  相似文献   

13.
Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics  相似文献   

14.
A new thermodynamic model is derived that describes both loading and pulse-response behavior of proteins in hydrophobic interaction chromatography (HIC). The model describes adsorption in terms of protein and solvent activities, and water displacement from hydrophobic interfaces, and distinguishes contributions from ligand density, ligand type and protein species. Experimental isocratic response and loading data for a set of globular proteins on Sepharose™ resins of various ligand types and densities are described by the model with a limited number of parameters. The model is explicit in ligand density and may provide insight into the sensitivity of protein retention to ligand density in HIC as well as the limited reproducibility of HIC data.  相似文献   

15.
    
Glucokinase (GK) plays a critical role in maintaining glucose homeostasis in the human liver and pancreas. In the liver, the activity of GK is modulated by the glucokinase regulatory protein (GKRP) which functions as a competitive inhibitor of glucose to bind to GK. Moreover, the inhibitory intensity of GKRP–GK is suppressed by fructose 1-phosphate (F1P), and reinforced by fructose 6-phosphate (F6P). Here, we employed a series of computational techniques to explore the interactions of fructose phosphates with GKRP. Calculation results reveal that F1P and F6P can bind to the same active site of GKRP with different binding modes, and electrostatic interaction provides a major driving force for the ligand binding. The presence of fructose phosphate severely influences the motions of protein and the conformational space, and the structural change of sugar phosphate influences its interactions with GKRP, leading to a large conformational rearrangement of loop2 in the SIS2 domain. In particular, the binding of F6P to GKRP facilitates the protruding loop2 contacting with GK to form the stable GK–GKRP complex. The conserved residues 179–184 of GKRP play a major role in the binding of phosphate group and maintaining the stability of GKRP. These results may provide deep insight into the regulatory mechanism of GKRP to the activity of GK.  相似文献   

16.
In this work, the all-atom (AA) force fields were set up for three kinds of dual amino-functionalized imidazolium-based ionic liquids (ILs), composed by cations with different alkyl chain length and amino acid anion [Gly]. The force field was based on our previous work and the default parameters were developed in this study. Molecular dynamics simulations were performed. Validation was carried out by comparing simulation densities with experimental data, and good agreement was obtained. Molar volume and heat capacity at constant pressure were predicted. Mean square displacements for these ILs were computed and these ILs were proved to move very slowly. It may be caused by hydrogen-bonded network between ions and the terminal azyl. To depict the microscopic structures of the ILs, many types of radial distribution functions were investigated. It is interesting to find that not only the cation and anion, but also the anions themselves will form hydrogen bonds.  相似文献   

17.
    
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18.
    
Molecular dynamics simulations were conducted to characterize the adsorption behavior of branched polyethylenimine (br‐PEI) on the surface of gold nanoparticles (AuNPs). We observed the preferential adsorption of br‐PEI on the [111] surface of AuNPs. Furthermore, br‐PEI maintained a flat arrangement on the surface and wrapped the AuNPs in a stable manner, thereby blocking the adsorption of H2O molecules and other free br‐PEI molecules. The model and computational results provide theoretical support for relevant experiments. Copyright © 2016 John Wiley & Sons, Ltd.  相似文献   

19.
20.
利用同源模建和分子动力学模拟,模建了细胞色素P450(CYP2s1)的三维结构.在模建结构的基础上,分析了活性位点的组成和结构,并进行了与小分子(维甲酸)的分子对接研究.研究结果表明,在由维甲酸和CYP2s1形成的复合物中,非键相互作用较强,其中,GLu411和Ala414是与维甲酸相互作用能最强的两个残基,对复合物的结合起重要作用.  相似文献   

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