Kinetic distance and kinetic maps from molecular dynamics simulation

Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine

Ultradiscrete kinks with supersonic speed in a layered crystal with realistic potentials

We develop a dynamical model of the propagating nonlinear localized excitations, supersonic kinks, in the cation layer in a silicate mica crystal. We start from purely electrostatic Coulomb interaction and add the Ziegler-Biersack-Littmark short-range repulsive potential and the periodic potential produced by other atoms of the lattice. This approach allows the construction of supersonic kinks which can propagate in the lattice within a large range of energies and velocities. The interparticle distances in the lattice kinks with high energy are physically reasonable values. The introduction of the periodic lattice potential results in the important feature that the kinks propagate with a single velocity and a single energy which are independent on the excitation conditions. The found kinks are ultra-discrete and can be described with the "magic wave number" $q\simeq 2\pi/3a$, which was previously revealed in the nonlinear sinusoidal waves and supersonic kinks in the Fermi-Pasta-Ulam lattice. The extreme discreteness of the supersonic kinks, with basically two particles moving at the same time, allows the interpretation of their double-kink structure. The energy of the supersonic kinks is between the possible source of $^{40}$K recoil in beta decay and the energy necessary for the ejection of an atom at the border as has been found experimentally.Comment: 14 pages, 15 figure

Phase diagram of a two-dimensional lattice gas model of a ramp system

Using Monte Carlo Simulation and fundamental measure theory we study the phase diagram of a two-dimensional lattice gas model with a nearest neighbor hard core exclusion and a next-to-nearest neighbors finite repulsive interaction. The model presents two competing ranges of interaction and, in common with many experimental systems, exhibits a low density solid phase, which melts back to the fluid phase upon compression. The theoretical approach is found to provide a qualitatively correct picture of the phase diagram of our model system.Comment: 14 pages, 8 figures, uses RevTex

Nonlinear waves in a chain of magnetically coupled pendula

A motivation for the study of reduced models like one-dimensional systems in Solid State Physics is the complexity of the full problem. In recent years our group has studied theoretically, numerically and experimentally wave propagation in lattices of nonlinearly coupled oscillators. Here, we present the dynamics of magnetically coupled pendula lattices. These macroscopic systems can model the dynamical processes of matter or layered systems. We report the results obtained for harmonic wave propagation in these media, and the different regimes of mode conversion into higher harmonics strongly influenced by dispersion and discreteness, including the phenomenon of acoustic dilatation of the chain, as well as some results on the propagation of localized waves i.e., solitons and kinks.Generalitat Valenciana APOSTD/2017/042Umiversitat Politècnica de València PAID-01-14Ministerio de Economía y Competitividad (MINECO), Spain FIS2015-65998-C2-2-PJunta de Andalucía 2017/FQM-28

Termoestabilización de proteínas de interés biotecnológico

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 12-12-2012Thermostability is a desired property for many biotechnological applications of enzymes because it allows an increase in their half-life at the working temperatures and produces a concomitant increase in the stability against organic solvents and detergents. Thermostable enzymes from thermophilic microorganisms are well adapted to such conditions, but not are always available or fulfill the role that the industry or specific applications require, leading to the development of methods to select thermostable variants from enzymes of mesophilic origin. Some of these methods rely on the deep knowledge of the structure-function relationships of the enzyme to design modifications that increase the thermostability. In other cases the methods of “directed evolution” mimics nature by selecting for a specific property (thermostability) among a high variety of random or semi-random mutants generated by in vitro or in vivo procedures. In directed evolution, the success of the selection depends on the capability to select over a huge amount of variants, and require either robotic system for the analysis of individual variants, or intermediate enrichment selection procedures to decrease the burden of selection. In this Thesis, we have applied the method of folding interference at high temperature in a thermophilic host (Thermus thermophilus) to select thermostable variants of two very different enzymes, a DNA polymerase form bacteriophage φ29, and the esterase I from Pseudomonas fluorescens (PFEI). The method is based on the expression in the thermophilic host of fusions between the target protein (N-terminal) and a thermostable kanamycin nucleotidyl transferase (C-terminal) as selectable reporter. In the first part of the experimental work, we isolated T. thermophilus deletion mutants defective in a major LonA-like protease, and checked their suitability as selection host, leading us to conclude that this protease is highly relevant to avoid toxicity of the fusions. In the second and third experimental sections, we isolated “folding-reinforced” mutants of the exonuclease and polymerase domains of the DNA polymerase of F29 and explained on structural ground their effects on stability. In the final experimental section, we went through the isolation of thermostable variants of the PFEI, and also were able to explain most of the observed effects on structural models. Some of the mutations obtained with both proteins are likely susceptible of patent protection. General conclusions about what can be expected for the general application of this method to isolate thermostable variants of any protein are discussed

Particle-based membrane model for mesoscopic simulation of cellular dynamics

We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending, and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model, and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems

Dispersal of transgenes through maize seed systems in Mexico.

ObjectivesCurrent models of transgene dispersal focus on gene flow via pollen while neglecting seed, a vital vehicle for gene flow in centers of crop origin and diversity. We analyze the dispersal of maize transgenes via seeds in Mexico, the crop's cradle.MethodsWe use immunoassays (ELISA) to screen for the activity of recombinant proteins in a nationwide sample of farmer seed stocks. We estimate critical parameters of seed population dynamics using household survey data and combine these estimates with analytical results to examine presumed sources and mechanisms of dispersal.ResultsRecombinant proteins Cry1Ab/Ac and CP4/EPSPS were found in 3.1% and 1.8% of samples, respectively. They are most abundant in southeast Mexico but also present in the west-central region. Diffusion of seed and grain imported from the United States might explain the frequency and distribution of transgenes in west-central Mexico but not in the southeast.ConclusionsUnderstanding the potential for transgene survival and dispersal should help design methods to regulate the diffusion of germplasm into local seed stocks. Further research is needed on the interactions between formal and informal seed systems and grain markets in centers of crop origin and diversification

Fructooligosaccharides and β-fructofuranosidase production by Aspergillus japonicus immobilized on lignocellulosic materials

This work describes the fructooligosaccharides (FOS) and β-fructofuranosidase (FFase) production from sucrose (200 g/l) by Aspergillus japonicus ATCC 20236 immobilized on different lignocellulosic materials including brewer's spent grain, wheat straw, corn cobs, coffee husks, cork oak, and loofa sponge. Transfructosylating (Ut) and hydrolyzing (Uh) activities of FFase were also determined. The FOS production and FFase activity ranged from 128.35 to 138.73 g/l, and 26.83 to 44.81 U/ml, respectively, for cells immobilized in the different carriers. Corn cobs was the best support material since gave the highest results of microorganism immobilization (1.49 g/g carrier), FOS and FFase production, with FOS productivity (6.61 g/l h) and yield (0.66 g/g based on total substrate; 0.73 g/g based on consumed substrate) higher than those obtained by free cells system. Moreover, the ratio Ut/Uh of FFase, parameter of importance for elevated FOS production, was greater for cells immobilized in corn cobs than for free cells. Such results demonstrated that corn cobs can be successfully used as carrier for immobilization of the fungus A. japonicus, for the production of FOS and FFase.Fundação para a Ciência e a Tecnologia (FCT

Colonization of Aspergillus japonicus on synthetic materials and application to the production of fructooligosaccharides

The ability of Aspergillus japonicus ATCC 20236 to colonize different synthetic materials (polyurethane foam, stainless steel sponge, vegetal fiber, pumice stones, zeolites, and foam glass) and to produce fructooligosaccharides (FOS) from sucrose (165 g/L) is described. Cells were immobilized in situ by absorption, through direct contact with the carrier particles at the beginning of fermentation. Vegetal fiber was the best immobilization carrier as A. japonicus grew well on it (1.25 g/g carrier), producing 116.3 g/L FOS (56.3 g/L 1-kestose, 46.9 g/L 1-nystose, and 13.1 g/L 1-β-fructofuranosyl nystose) with 69% yield (78% based only in the consumed sucrose amount), giving also elevated activity of the β-fructofuranosidase enzyme (42.9 U/mL). In addition, no loss of material integrity, over a 2 day-period, was found. The fungus also immobilized well on stainless steel sponge (1.13 g/g carrier), but in lesser extents on polyurethane foam, zeolites, and pumice stones (0.48, 0.19, and 0.13 g/g carrier, respectively), while on foam glass no cell adhesion was observed. When compared with the FOS and β-fructofuranosidase production by free A. japonicus, the results achieved using cells immobilized on vegetal fiber were closely similar. It was thus concluded that A. japonicus immobilized on vegetal fiber is a potential alternative for high production of FOS at industrial scale.Fundação para a Ciência e a Tecnologia (FCT

An efficient multi-scale Green’s function reaction dynamics scheme

Molecular Dynamics-Green’s Function Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction- diffusion dynamics that is suited for systems involving low particle densities. Particles in a low-density region are just diffusing and not interacting. In this case, one can avoid the costly integration of microscopic equations of motion, such as molecular dynamics (MD), and instead turn to an event-based scheme in which the times to the next particle interaction and the new particle positions at that time can be sampled. At high (local) concentrations, however, e.g., when particles are interacting in a nontrivial way, particle positions must still be updated with small time steps of the microscopic dynamical equations. The efficiency of a multi-scale simulation that uses these two schemes largely depends on the coupling between them and the decisions when to switch between the two scales. Here we present an efficient scheme for multi-scale MD-GFRD simulations. It has been shown that MD-GFRD schemes are more efficient than brute-force molecular dynamics simulations up to a molar concentration of 102 μM. In this paper, we show that the choice of the propagation domains has a relevant impact on the computational performance. Domains are constructed using a local optimization of their sizes and a minimal domain size is proposed. The algorithm is shown to be more efficient than brute-force Brownian dynamics simulations up to a molar concentration of 103 μM and is up to an order of magnitude more efficient compared with previous MD-GFRD schemes