Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation.

Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyze a model for quorum-sensing triggered biofilm initiation.

A computational model for microbial colonization of an antifouling surface.

Biofouling of marine surfaces such as ship hulls is a major industrial problem. Antifouling (AF) paints delay the onset of biofouling by releasing biocidal chemicals. We present a computational model for microbial colonization of a biocide-releasing AF surface.

Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov State Models and Transition Networks.

Protein disorder and aggregation play significant roles in the pathogenesis of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. The end products of the aggregation process in these diseases are highly structured amyloid fibrils. Though in most cases, small, soluble oligomers formed during amyloid aggregation are the toxic species.

Phenotypic delay in the evolution of bacterial antibiotic resistance: Mechanistic models and their implications.

Phenotypic delay-the time delay between genetic mutation and expression of the corresponding phenotype-is generally neglected in evolutionary models, yet recent work suggests that it may be more common than previously assumed. Here, we use computer simulations and theory to investigate the significance of phenotypic delay for the evolution of bacterial resistance to antibiotics. We consider three mechanisms which could potentially cause phenotypic delay: effective polyploidy, dilution of antibiotic-sensitive molecules and accumulation of resistance-enhancing molecules.

Receptor crosstalk improves concentration sensing of multiple ligands.

Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway.

Growth-dependent drug susceptibility can prevent or enhance spatial expansion of a bacterial population.

As a population wave expands, organisms at the tip typically experience plentiful nutrients while those behind the front become nutrient-depleted. If the environment also contains a gradient of some inhibitor (e.g.

Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly.

Markov state models have become popular in the computational biochemistry and biophysics communities as a technique for identifying stationary and kinetic information of protein dynamics from molecular dynamics simulation data. In this paper, we extend the applicability of automated Markov state modeling to simulation data of molecular self-assembly and aggregation by constructing collective coordinates from molecular descriptors that are invariant to permutations of molecular indexing. Understanding molecular self-assembly is of critical importance if we want to deepen our understanding of neurodegenerative diseases where the aggregation of misfolded or disordered proteins is thought to be the main culprit.

On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations.

Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ peptide and two of its mutants: Aβ(F19V,F20V), which does not form fibrils, and Aβ(F19L) which forms fibrils faster than the wild type.

Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains.

Antibody light chain amyloidosis is a rare disease caused by fibril formation of secreted immunoglobulin light chains (LCs). The huge variety of antibody sequences puts a serious challenge to drug discovery. The green tea polyphenol epigallocatechin-3-gallate (EGCG) is known to interfere with fibril formation in general.

Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins.

Intrinsically disordered proteins are essential for biological processes such as cell signalling, but are also associated to devastating diseases including Alzheimer's disease, Parkinson's disease or type II diabetes. Because of their lack of a stable three-dimensional structure, molecular dynamics simulations are often used to obtain atomistic details that cannot be observed experimentally. The applicability of molecular dynamics simulations depends on the accuracy of the force field chosen to represent the underlying free energy surface of the system.

Advances in the Simulation of Protein Aggregation at the Atomistic Scale.

Protein aggregation into highly structured amyloid fibrils is associated with various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also have normal biological functions and, in the future, could be used as the basis for novel nanoscale materials. However, a full understanding of the physicochemical forces that drive protein aggregation is still lacking.

Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations.

Amyloids are associated with diseases, including Alzheimer's, as well as functional roles such as storage of peptide hormones. It is still unclear what differences exist between aberrant and functional amyloids. However, it is known that soluble oligomers formed during amyloid aggregation are more toxic than the final fibrils.