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Whether recent updates and new releases of atomistic force fields can model the structural and dynamical properties of proteins containing both folded and partially disordered domains is still unclear. To address this fundamental question, we tested eight recently released force fields against our set of nuclear magnetic resonance (NMR) observables for a complex and medically relevant system, the major factor VIII binding region on von Willebrand factor. This biomedically important region comprises both a folded and a partially structured domain. By using an enhanced sampling technique (temperature replica-exchange molecular dynamics simulations), we find that some force fields indeed rise to the challenge and capture the structural and dynamical features of the NMR ensemble and, therefore, are the appropriate choice for simulations of proteins with partially structured domains. What is more, we show that only such force fields can qualitatively capture the effects of a pathogenic mutation on the structural ensemble.
This article was published in the following journal.
Name: The journal of physical chemistry letters
The application of molecular dynamics simulations to study the folding and dynamics of peptides has attracted a lot of interest in the last couple of decades. Following the successful prediction of th...
Significant improvements have been made to the OPLS-AA force field for modeling RNA. New torsional potentials were optimized based on DFT scans at the ωB97X-D/6-311++G(d,p) level for potential energy...
Molecular simulations see widespread use in calculating various physical properties of interest, with a key goal being predictive molecular design. These simulations, including molecular dynamics (MD)...
A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to ha...
The article describes a GROMOS force field parameter set for molecular dynamics simulations of furanose carbohydrates. The proposed united-atom force field is designed and validated with respect to th...
New markers of viral activity are now under investigation. Aim of the study is to investigate the efficacy of new antiretroviral drugs by monitoring HIV-DNA dynamics in HIV-positive popula...
Under the circumstances that appropriate first-choice guidewires for percutaneous coronary intervention (PCI) for chronic total occlusion (CTO) have yet to be established, the objective of...
The purpose of this study is to evaluate a handheld Colonoscopy Force Monitor(CFM™), a push-pull force and torque measuring device, that grips the shaft of the colonoscope and wirelessly...
The objective of this prospective study is to confirm safety and performance of N-Force Screws augmented with N-Force Blue applied in intracapsular proximal femur fracture treatment.
Inducing a systematic perturbation forces on the hand during arm reaching movement may improve adaptation. Error-augmentation (EA) training is relatively new concept in motor learning inte...
The rotational force about an axis that is equal to the product of a force times the distance from the axis where the force is applied.
Condition in which no acceleration, whether due to gravity or any other force, can be detected by an observer within a system. It also means the absence of weight or the absence of the force of gravity acting on a body. Microgravity, gravitational force between 0 and 10 -6 g, is included here. (From NASA Thesaurus, 1988)
The interdisciplinary field concerned with the development and integration of behavioral and biomedical science, knowledge, and techniques relevant to health and illness and the application of this knowledge and these techniques to prevention, diagnosis, treatment, and rehabilitation.
The force applied by the masticatory muscles in dental occlusion.
Force exerted when using the index finger and the thumb. It is a test for determining maximum voluntary contraction force.