323,082 research outputs found
Application of the Poisson-Nernst-Planck theory with space-dependent diffusion coefficients to KcsA
No full textThe Poisson-Nernst-Planck electrodiffusion theory serves to compute charge fluxes and is here applied to the ion current through a protein channel. KcsA was selected as an example because of the abundance of experimental and theoretical data. The potassium channels MthK and KvAP were used as templates to define two open channel models for KcsA. Channel boundary surfaces and protein charge distributions were defined according to atomic radii and partial atomic charges. To establish the sensitivity of the results to these parameters, two different sets were used. Assigning the potassium diffusion coefficients equal to the value for free-diffusion in water (1.96 x 10(-9) m(2)/s), the computed currents overestimated the experimental data. Ion distributions inside the channel suggest that the overestimate is not due to an excess of charge shielding. A good agreement with the experimental data was achieved by reducing the potassium diffusion coefficient inside the channel to 1.96 x 10(-10) m(2)/s, a value of substantial motility but nonetheless in accord with the intuitive notion that the channel has a high affinity for the ions and therefore slows them down. These results are independent of the open channel model and the parameterization adopted for atomic radii and partial atomic charges. The method offers a reliable estimate of the channel current with low computational effort
The costly process of creating a cavity in n-octanol
No full textFree-energy perturbation calculations are used to evaluate the free energy of cavity formation in n-octanol. A detailed theoretical analysis of the procedure is given and some limiting value phenomena are discussed. The data become subject to a three-parameter fit and a revised formulation of the popular approach due to Pierotti of calculating cavitation free energies is given. Pierotti's approach is based on the equation derived from scaled particle theory (SPT) by Reiss et al. [(2000) J. Chem. Phys. 31:369-380]. The revision of Pierotti's approach has the important advantage of being completely independent of the solvent hard-sphere radius, an empirical parameter in the standard procedure, which is hard to define in a uniformly valid way
Role of the intracellular cavity in potassium channel conductivity
No full textThe role of several fragments of the potassium channel KcsA has been examined by the Poisson-Nernst-Planck (PNP) theory. The efficiency of the computational method allowed comparing a large number of channel models, with different intracellular gate openings, partial atomic charges, and amino acid sequences. Perhaps counter-intuitively, the calculated ion current decreases when the mean radius of the entrance cavity increases. Widening of the vestibule, in fact, increases the volume accessible to water, which is the volume with a high dielectric constant. In turn, water screens the attractive charges of the P-loop backbone. The backbone charges of the M2 helixes instead oppose the entrance of potassium ions through a complicated mechanism that can be separated in the activity of two interfering dipoles. The conductance of the KcsA models increased when two neutral residues in M2 were mutated to glutamic acid, in agreement with experimental results (Brelidze, T. I.; Niu, X.; Magleby, K. L. PNAS 2003, 100, 9017-9022). As a general conclusion, a relation between channel conductance and potassium concentration in the intracellular cavity emerged. Although the ion transport is the result of the fine balance of a number of different effects, the experimental results can be reproduced quantitatively only on the basis of electrostatic forces, which are the only driving forces modeled by the PNP theory
A numerical solver of 3D Poisson and Nernst-Planck equations, application to ion channel conduction
No full textRecent results of X-Ray crystallography have provided important information for functional studies of membrane ion channels based on computer simulations. Because of the large number of atoms that constitute the channel proteins, it is prohibitive to approach functional studies using molecular dynamic methods. To overcome the current computational limit we propose a novel approach based on the Poisson, Nernst, Planck electrodiffusion theory. The proposed numerical method allows the quick computation of ion flux through the channel, starting from its 3D structure. We applied the method to the KcsA potassium channel obtaining a good accordance with the experimental data
Modeling the stability and the motion of DNA nucleobases on the gold surface
No full textWe simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considere
Stochastic modelling of13c nmr spin relaxation experiments in oligosaccharides
No full textA framework for the stochastic description of relaxation processes in flexible macromolecules including dissipative effects has been recently introduced, starting from an atomistic view, describing the joint relaxation of internal coordinates and global degrees of freedom, and depending on parameters recoverable from classic force fields (energetics) and medium modelling at the continuum level (friction tensors). The new approach provides a rational context for the interpretation of magnetic resonance relaxation experiments. In its simplest formulation, the semi-flexible Brownian (SFB) model has been until now shown to reproduce correctly correlation functions and spectral densities related to orientational properties obtained by direct molecular dynamics simulations of peptides. Here, for the first time, we applied directly the SFB approach to the practical evaluation of high-quality13C nuclear magnetic resonance relaxation parameters, T1 and T2, and the heteronuclear NOE of several oligosaccharides, which were previously interpreted on the basis of refined ad hoc modelling. The calculated NMR relaxation parameters were in agreement with the experimental data, showing that this general approach can be applied to diverse classes of molecular systems, with the minimal usage of adjustable parameters
Advanced computational tools for the interpretation of magnetic resonance spectroscopies
No full textElectron and nuclear magnetic spectroscopies are powerful tools for studying molecular dynamics,
being particularly sensitive to motions with relaxation times in the range of 10−9
- 10−6 s. This time window includes rigid body motions in fluids and ”soft” internal motions
of molecules. Moreover, dynamics in this range comprehend proteins internal motions
responsible for relevant chemical-physical properties, like substrate recognition, activity and
folding.
In a typical electron spin resonance (ESR) experiment molecular motions affect considerably
the shape of the spectral line. In a nuclear magnetic resonance (NMR) experiment characteristic
relaxations times of the spin magnetization, i.e. T1, T2 and NOE, are directly affected
by internal mobility.
The aim of this Ph.D. work is the implementation of integrated theoretical / computational
methodologies for characterization of dynamical properties of molecules gathered from ESR
and NMR measurements. The starting point is a ”time coarse-graining” procedure that leads
to simplified models in which we introduce only dynamical characteristics that are relevant
to the physical observables considered. In particular, stochastic models are employed, based
on a number of structural parameters which are calculated. The idea is to treat these parameters
at atomistic and / or mesoscopic level depending on their nature.
Software packages have been developed, comprehending E-SpiReS (Electron Spin Resonance
Simulation) for cw-ESR simulations, C++OPPS (COupled Probe Protein Smoluchowski) for
NMR simulations and DITE (DIffusion TEnsor) for the evaluation of dissipative properties
of molecules. These programs have been built as user-friendly tools targeted for use by
experimentalists, as a kind of in silico extension of the laboratory equipment.Tecniche efficaci nello studio della dinamica molecolare sono le spettroscopie di risonanza elettronica e nucleare, essendo particolarmente sensibili a moti caratterizzati da scale dei tempi nell'intervallo da 10^-9 a 10^-6 s, nel quale rientrano sia i moti globali (di corpo rigido), sia le dinamiche interne di molecole in soluzione. E' da notare che questa finestra comprende anche la dinamica delle proteine, responsabile di proprieta' chimico-fisiche molto importanti, quali il riconoscimento del substrato, l'attivita' ed il folding.
Tipicamente, in un esperimento di risonanza di spin elettronico (RSE) i moti molecolari sono responsabili dell'allargamento inomogeneo delle righe spettrali.
Per quanto riguarda la risonanza magnetica nucleare (RMN), invece, la dinamica molecolare influisce sui rilassamenti T1, T2 e NOE.
Lo scopo di questo lavoro e' l'implementazione di metodologie integrate teorico / computazionali per la caratterizzazione della dinamica molecolare a partire da misure RSE e RMN. In particolare, si proiettano i moti non importanti (''time coarse-graining''), ottenendo modelli per la dinamica relativamente semplici, che descrivono esclusivamente i moti rilevanti rispetto all'osservabile fisico in esame. In particolare, si impiegano modelli stocastici nei quali intervengono anche parametri strutturali che devono essere calcolati. Questi ultimi sono descritti a livello atomistico e / o mesoscopico in base alla loro natura.
Sono stati sviluppati tre nuovi programmi: E-SpiReS (Electron Spin Resonance Simulation) per la simulazione di spettri RSE in onda continua, C++OPPS (COupled Protein Probe Smoluchowski) per simulazioni di misure di RMN e DITE (DIffusion TEnsor) per il calcolo di proprieta' dissipative di molecole con gradi di liberta' interni. Nell'implementazione dei programmi si e' fatto attenzione alla semplicita' d'uso, occupandosi anche dello sviluppo di interfacce grafiche, con l'obiettivo di affiancare i programmi alla strumentazione di laboratorio, come una sorta di estensione ''in silico'' della stessa
Studio Raman e SERS dei complessi metallici di Ibuprofen.
No full textL'Ibuprofen è un principio attivo del gruppo dei farmaci non steroidei dotati di proprietà anti infiammatorie, in cui il sito di interazione attraverso cui si sviluppano le proprietà farmacologiche è costituito dal gruppo carbossilato, che può anche essere disponibile per interazioni legante-metallo. L'interesse per lo studio strutturale dei complessi metallici deriva dall'osservazione che la complessazione con ioni metallici può favorire il trasporto del farmaco, rendendolo più efficace; inoltre alcuni autori riportano che i complessi di antiinfiammatori con il Cu(II) presentano un effetto anti-ulcera. Gli spettri Raman dei complessi metallici di Ibu hanno diversa struttura: il complesso Cu-Ibu presenta struttura bidentata a ponte (si osservano infatti le bande attribuite al legame Cu-O e del ponte Cu-Cu2), mentre il complesso Ibu-Zn ha una struttura bidentata 2:1 semplice. La tecnica 'Surface Enhanced Raman Spectroscopy' (SERS), consentendo una notevole amplificazione dell'intensità degli spettri Raman, estende l'uso delle spettroscopie vibrazionali alle concentrazioni bioattive dei farmaci (ppm) in soluzione. Gli spettri SERS mostrano bande intense nella regione 1350-1600 cm-1, attribuibili ai modi vibrazionali degli anelli aromatici e del gruppo COO-. Si nota che gli spettri Raman dei solidi sono alquanto diversi da quelli SERS degli stessi composti, poiché solo le bande dovute alle vibrazioni dei gruppi direttamente interagenti con la superficie delle particelle colloidali di Ag sono amplificate e questo spiega la relativa semplicità degli spettri SERS. L'elevata amplificazione delle bande dovute allo ione carbossilato e agli anelli aromatici conferma che, per tutti i composti considerati, l'interazione con la superfìcie di Ag è dovuta alle coppie di elettroni degli atomi di ossigeno e che le molecole si chemiadsorbono sulla superficie delle particelle di colloide
- …
