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Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson–Boltzmann theory and its modifications
TLDR
This work is a review of the Poisson–Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding, and discusses the conventional PB equation, the corresponding functionals of the electrostatic free energy, including a connection to DFT.
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Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.
TLDR
Brownian dynamics simulations in a coarse-grained model are applied to study the gated association rate constants of HIV-1 proteases and drugs and suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant open less frequently, resulting in a lower gated rate constant.
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Binding Pathways of Ligands to HIV‐1 Protease: Coarse‐grained and Atomistic Simulations
TLDR
This is the first molecular dynamics simulation of modeling the association of a ligand with the protease and it is found that a protease substrate successfully binds to the protein when the flaps are fully open.
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Thermodynamic linkage between the binding of protons and inhibitors to HIV‐1 protease
TLDR
Computations and measurements related to changes in protonation and to the thermodynamic linkage between protonated and inhibition are presented and implications for the accurate calculation of pKas in complex protein environments are presented.
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Secondary structures of native and pathogenic huntingtin N-terminal fragments.
TLDR
It is found that corresponding regions in both fragments fold to similar secondary structures; the headpiece and polyQ stretch adopt mainly α-helical conformations, and polyP(11) forms the PP II-type helix.
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Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study.
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Brownian dynamics simulations on CPU and GPU with BD_BOX
TLDR
A software package, BD_BOX, for multiscale Brownian dynamics simulations, which can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse‐grained bead models.
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Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.
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Dependency Map of Proteins in the Small Ribosomal Subunit
TLDR
The results show that by blocking one out of this set of proteins, the association of other proteins is eventually reduced, thus reducing the translation efficiency even more, and discusses the implications on how to target the ribosomal assembly most effectively by suggesting six proteins as targets for mutations or other hindering of their binding.
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Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions
TLDR
This work investigates the proteolytic activity of the human immunodeficiency virus type 1 protease (HIV-1 PR) under non-crowded and crowded conditions and finds that crowding agents affect the kinetic parameters of the HIV-1PR catalyzed reaction by increasing the Michaelis–Menten constant and decreasing the maximum velocity.
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