A structurally relevant coarse-grained model for cholesterol

Detailed atomistic computer simulations are now widely used to study biological membranes, including increasingly mixed lipid systems that involve, for example, cholesterol, which is a key membrane lipid. Typically, simulations of these systems start from a preassembled bilayer because the timescale on which self-assembly occurs in mixed lipid systems is beyond the practical abilities of fully atomistic simulations. To overcome this limitation and study bilayer self-assembly, coarse-grained models have been developed. Although there are several coarse-grained models for cholesterol reported in the literature, these generally fail to account explicitly for the unique molecular features of cholesterol that relate to its function and role as a membrane lipid. In this work, we propose a new coarse-grained model for cholesterol that retains the molecule's unique features and, as a result, can be used to study crystalline structures of cholesterol. In the development of the model, two levels of coarse-graining are explored and the importance of retaining key molecular features in the coarse-grained model that are relevant to structural properties is investigated.     

New coarse-grained DNA model

A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis. The model has been shown to rather well reproduce the DNA structure under low and room temperatures. The Young's and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of micros) and for simulating their interactions with other structures.     

New coarse-grained DNA model

A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis. The model has been shown to rather well reproduce the DNA structure under low and room temperatures. The Young’s and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of μs) and for simulating their interactions with other structures.     

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2-angstroms backbone root-mean-square distance from the corresponding NMR structures. The minimum root-mean-square distance of Trp-cage conformations in simulations can be <1 angstroms. Our findings suggest that, at least in the case of Trp-cage, a detailed all-atom protein model with a molecular mechanics force field is not necessary to reach the native state of a protein. Our results also suggest that the success of folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulation studies may be mainly due to the special stabilizing features specific to this miniprotein.     

Describing force-induced bone growth and adaptation by a mathematical model

This work proposes a mathematical model that qualitative describes the process of mechanically force-induced bone growth and adaptation. The mathematical model includes osteocytes as the key interfacing layer connecting tissue, cellular and molecular signaling levels. Specifically, in the presence of an increase in the mechanical stimuli, osteocytes respond by mechano-transduction releasing the local factors nitric oxide (NO) and prostaglandin E(2) (PGE(2)). These local factors act as the signaling recruitment signals for bone cells progenitors and influence the coupling activity among osteoblasts and osteoclasts during the process of bone remodeling. The model is in agreement with qualitative observations found in the literature concerning the process of bone adaptation and the cellular interactions during a local bone remodeling cycle induced by mechanical stimulation.     

Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data

Simple coarse-grained models, such as the Gaussian network model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to define residue interactions and introducing more than one interaction parameter between residues. We use B-factors from 98 ultra-high resolution (相似文献   

A model for the measurement of whole-body protein turnover incorporating a protein pool with lifetime kinetics.

The hypothesis is proposed that the body contains a pool of protein turning over by lifetime rather than traditional first-order kinetics. The basis of the hypothesis is the observation of a step in the labelling curve or urinary ammonia during constant infusion of [15N]glycine. A four pool model has been constructed with different values for the rate of uptake of tracer into the lifetime pool; the calculated curves of tracer concentration show a step quite similar to that observed experimentally. It is concluded that it is possible, from an experimental curve, to derive an approximate estimate of the relative flux to the lifetime protein pool. Some suggestions are proposed for the physiological nature of this pool.     

A chemical kinetics model for microtubule oscillations

A model for microtubule oscillations is presented based on a set of chemical reaction equations. The rate constants for these reactions are largely determined from experimental data. The plots of assembled tubulin and the phase diagram for assembly are compared with the experimental findings and are found to agree quite well. Copyright 1999 Academic Press.     

Two-component coarse-grained molecular-dynamics model for the human erythrocyte membrane

We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membrane under shearing and found that at a low shear strain rate, the developed shear stress was due mainly to the spectrin network, whereas the viscosity of the lipid bilayer contributed to the resulting shear stress at higher strain rates. In addition, we investigated the effects of a reduced spectrin network connectivity on the shear modulus of the membrane.     

A coarse-grained force field for Protein-RNA docking

The awareness of important biological role played by functional, non coding (nc) RNA has grown tremendously in recent years. To perform their tasks, ncRNA molecules typically unite with protein partners, forming ribonucleoprotein complexes. Structural insight into their architectures can be greatly supplemented by computational docking techniques, as they provide means for the integration and refinement of experimental data that is often limited to fragments of larger assemblies or represents multiple levels of spatial resolution. Here, we present a coarse-grained force field for protein-RNA docking, implemented within the framework of the ATTRACT program. Complex structure prediction is based on energy minimization in rotational and translational degrees of freedom of binding partners, with possible extension to include structural flexibility. The coarse-grained representation allows for fast and efficient systematic docking search without any prior knowledge about complex geometry.     

A coarse-grained model for PCL: conformation,self-assembly of MePEG-b-PCL amphiphilic diblock copolymers

Poly-ε-caprolactone (PCL) is a biodegradable hydrophobic polyester that has been widely used in medical devices, tissue engineering and nanoparticle-based drug delivery. Coarse-grained molecular dynamics (CGMD) has been employed to study and gain insights into the conformational, structural and self-assembly behaviour of polymers, lipids and amphiphilic macromolecules. In this work, we developed a model for PCL within the framework of the MARTINI coarse-grained force field. The non-bonded interactions were based on the existing MARTINI bead types, while the bonded interactions were mapped onto a PCL rendition obtained from atomistic simulations. The model accurately reproduces the structural and dynamic properties of the PCL homopolymer and shows very reasonable temperature and solvent transferability. We also studied self-assembly of MePEG-b-PCL linear diblock copolymers using an existing MARTINI model for MePEG (Methoxy Polyethylene glycol), by analysing the critical micelle concentration (CMC), as well as the shape, size and morphology of the nano-polymeric micelles. We obtained excellent agreement of the CMC, while the size was under-predicted compared to experimental data. This robust model paves the way for CGMD modelling of PCL and serves as a starting point for future designs of PCL-related polymeric systems .     

A three-state model for connexin37 gating kinetics

The gating behavior of human connexin 37 (hCx37) is unaffected by the nature of the bathing monovalent (for Na, K, Rb). It is modified by [Mg] in the millimolar range. For fitting the kinetics, we propose a simple extension to three states of the canonical 2-state model of the hemichannel. The extra closed state allows for some immobilization of a hemichannel at high transjunctional voltages. The model is reasonably efficient at fitting data at various voltage protocols. Interpreting the fits of the data at different [Mg] is consistent with a binding site for Mg.     

A model of DSB-repair kinetics

A model of repair kinetics of DSB based on a step-by-step removal of individual double-strand breaks inside an autonomous repair unit is proposed and compared with the alternative model commonly used in modelling repair kinetics, which is based on an assumption of stochastic removal of cellular lesions. The former model seems to be preferred by the recently published experimental data displaying the time decrease of average DSB number per cell in irradiated Saccharomyces cerevisiae (strain 211 B) held in non-growth conditions.     

A mathematical model for germinal centre kinetics and affinity maturation

We present a mathematical model which reproduces experimental data on the germinal centre (GC) kinetics of the primed primary immune response and on affinity maturation observed during the reaction. We show that antigen masking by antibodies which are produced by emerging plasma cells can drive affinity maturation and provide a feedback mechanism by which the reaction is stable against variations in the initial antigen amount over several orders of magnitude. This provides a possible answer to the long-standing question of the role of antigen reduction in driving affinity maturation. By comparing model predictions with experimental results, we propose that the selection probability of centrocytes and the recycling probability of selected centrocytes are not constant but vary during the GC reaction with respect to time. It is shown that the efficiency of affinity maturation is highest if clones with an affinity for the antigen well above the average affinity in the GC leave the GC for either the memory or plasma cell pool. It is further shown that termination of somatic hypermutation several days before the end of the germinal centre reaction is beneficial for affinity maturation. The impact on affinity maturation of simultaneous initiation of memory cell formation and somatic hypermutation vs. delayed initiation of memory cell formation is discussed.     

A phenomenological model for cell and nucleus deformation during cancer metastasis

Cell migration plays an essential role in cancer metastasis. In cancer invasion through confined spaces, cells must undergo extensive deformation, which is a capability related to their metastatic potentials. Here, we simulate the deformation of the cell and nucleus during invasion through a dense, physiological microenvironment by developing a phenomenological computational model. In our work, cells are attracted by a generic emitting source (e.g., a chemokine or stiffness signal), which is treated by using Green’s Fundamental solutions. We use an IMEX integration method where the linear parts and the nonlinear parts are treated by using an Euler backward scheme and an Euler forward method, respectively. We develop the numerical model for an obstacle-induced deformation in 2D or/and 3D. Considering the uncertainty in cell mobility, stochastic processes are incorporated and uncertainties in the input variables are evaluated using Monte Carlo simulations. This quantitative study aims at estimating the likelihood for invasion and the length of the time interval in which the cell invades the tissue through an obstacle. Subsequently, the two-dimensional cell deformation model is applied to simplified cancer metastasis processes to serve as a model for in vivo or in vitro biomedical experiments.     

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

Background  

Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.