Search results for "Biomolecule"
showing 10 items of 666 documents
Computer simulation of bottle-brush polymers with flexible backbone: good solvent versus theta solvent conditions.
2011
By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \le N \le 40$, backbone chain lengths are in the range $50 \le N_b \le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of …
Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase
2015
Enzymes are the catalysts used by living organisms to accelerate chemical processes under physiological conditions. In this chapter, we illustrate the current view about the origin of their extraordinary rate enhancement based on molecular simulations and, in particular, on methods based on the combination of Quantum Mechanics and Molecular Mechanics potentials which provide a solution to treat the chemical reactivity of these large and complex molecular systems. Computational studies on Dihydrofolate Reductase have been selected as a conductor wire to present the evolution and difficulties to model chemical reactivity in enzymes. The results discussed here show that experimental observatio…
Biomolecule-corona formation confers resistance of bacteria to nanoparticle-induced killing: Implications for the design of improved nanoantibiotics
2018
Abstract Multidrug-resistant bacterial infections are a global health threat. Nanoparticles are thus investigated as novel antibacterial agents for clinical practice, including wound dressings and implants. We report that nanoparticles' bactericidal activity strongly depends on their physical binding to pathogens, including multidrug-resistant primary clinical isolates, such as Staphylococcus aureus , Klebsiella pneumoniae or Enterococcus faecalis . Using controllable nanoparticle models, we found that nanoparticle-pathogen complex formation was enhanced by small nanoparticle size rather than material or charge, and was prevented by 'stealth' modifications. Nanoparticles seem to preferentia…
Rigid versus Flexible Protein Matrix: Light-Harvesting Complex II Exhibits a Temperature-Dependent Phonon Spectral Density
2018
Dynamics-function correlations are usually inferred when molecular mobility and protein function are simultaneously impaired at characteristic temperatures or hydration levels. In this sense, excitation energy transfer in the photosynthetic light-harvesting complex II (LHC II) is an untypical example because it remains fully functional even at cryogenic temperatures relying mainly on interactions of electronic states with protein vibrations. Here, we study the vibrational and conformational protein dynamics of monomeric and trimeric LHC II from spinach using inelastic neutron scattering (INS) in the temperature range of 20-305 K. INS spectra of trimeric LHC II reveal a distinct vibrational …
The Structure of Cholesterol in Lipid Rafts
2014
Rafts, or functional domains, are transient nano- or mesoscopic structures in the plasma membrane and are thought to be essential for many cellular processes such as signal transduction, adhesion, trafficking and lipid/protein sorting. Observations of these membrane heterogeneities have proven challenging, as they are thought to be both small and short-lived. With a combination of coarse-grained molecular dynamics simulations and neutron diffraction using deuterium labeled cholesterol molecules we observe raft-like structures and determine the ordering of the cholesterol molecules in binary cholesterol-containing lipid membranes. From coarse-grained computer simulations, heterogenous membra…
Overview of the Evolution of Silica-Based Chromo-Fluorogenic Nanosensors
2019
[EN] This review includes examples of silica-based, chromo-fluorogenic nanosensors with the aim of illustrating the evolution of the discipline in recent decades through relevant research developed in our group. Examples have been grouped according to the sensing strategies. A clear evolution from simply functionalized materials to new protocols involving molecular gates and the use of highly selective biomolecules such as antibodies and oligonucleotides is reported. Some final examples related to the evolution of chromogenic arrays and the possible use of nanoparticles to communicate with other nanoparticles or cells are also included. A total of 64 articles have been summarized, highlight…
Non-equilibrium Markov state modeling of periodically driven biomolecules
2019
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external p…
Infrared nanospectroscopic mapping of DNA molecules on mica surface
2022
Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying AFM-IR technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the IR-AFM investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of IR-AFM mapping modalities with corres…
Monte Carlo Simulations in Polymer Science
2012
Monte Carlo methods are useful for computing the statistical properties of both single macromolecules of various chemical architectures and systems containing many polymers (solutions, melts, blends, etc.). Starting with simple models (lattice models such as the self-avoiding walk or the bond fluctuation model, as well as coarse-grained or chemically realistic models in the continuum) various algorithms exist to generate conformations typical for thermal equilibrium, but dynamic Monte Carlo methods can also model diffusion and relaxation processes (as described by the Rouse and the reptation models for polymer melt dynamics). Limitations of the method are explained, and also the measures to…
Shear Modulus of an Irreversible Diblock Copolymer Network from Self-Consistent Field Theory
2019
Using self-consistent field theory, we investigate the stretching-induced microphase separation in an irreversibly cross-linked polymer network composed of diblock copolymer chains and estimate its...