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Phosphorylated proteins take part in many signaling pathways and play a key role in homeostasis regulation. The all-atom force fields enable us to study systems containing phosphorylated proteins, but they are limited to short time scales. In this paper we report the extension of the physics-based coarse-grained UNRES force field to treat systems with phosphorylated amino-acid residues. To derive the respective potentials, appropriate physics-based analytical expressions were fitted to the potentials of mean force of systems modeling phosphorylated amino-acid residues computed in our previous work and implemented in UNRES. The extended UNRES performed well in ab initio simulations of two miniproteins containing phosphorylated residues, strongly suggesting that realistic large-scale simulations of processes involving phosphorylated proteins, especially signaling processes, are now possible.
This article was published in the following journal.
Name: The journal of physical chemistry. B
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Large, twisted, and fused conjugated molecular architectures have begun to appear more prominently in the organic semiconductor literature. From a modeling perspective, such structures present a chall...
Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions...
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Molecular dynamics represents a key enabling technology for applications ranging from biology to the development of new materials. However, many real-world applications remain inaccessible to fully re...
The study was performed to investigate the effects of the consumption of black currant seed press residues, which were baked into bread.
The primary objective of the study is to show that ventilation heterogeneity identified by hyperpolarized helium-3 lung MRI is prevalent children with poorly controlled asthma despite guid...
A randomized controlled single-blind clinical trial was performed, in 32 patients diagnosed with peritoneal carcinomatosis from epithelial ovarian cancer, who underwent radical surgery-per...
The main objective of Trial Parts 1 and 2 is to investigate the relative bioavailability of two tablet strengths (low dose and high dose) of the intended Commercial Formulation of BI 73035...
Objectives: Primary: - To evaluate the association of the probability of increase in phosphorylation of platelet-derived growth factor receptor (PDGFR) of > 0.5 in peripher...
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
An aspect of protein kinase (EC 184.108.40.206) in which serine residues in protamines and histones are phosphorylated in the presence of ATP. EC 220.127.116.11.
Theoretical models simulating behavior or activities in nursing, including nursing care, management and economics, theory, assessment, research, and education. Some examples of these models include Orem Self-Care Model, Roy Adaptation Model, and Rogers Life Process Model.
A dsRNA-activated cAMP-independent protein serine/threonine kinase that is induced by interferon. In the presence of dsRNA and ATP, the kinase autophosphorylates on several serine and threonine residues. The phosphorylated enzyme catalyzes the phosphorylation of the alpha subunit of EUKARYOTIC INITIATION FACTOR-2, leading to the inhibition of protein synthesis.
A principle of estimation in which the estimates of a set of parameters in a statistical model are those quantities minimizing the sum of squared differences between the observed values of a dependent variable and the values predicted by the model.