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New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute(More)
Aspartate transcarbamylase (ATCase) initiates the pyrimidine biosynthetic pathway in Escherichia coli. Binding of aspartate to this allosteric enzyme induces a cooperative transition between the tensed (T) and relaxed (R) states of the enzyme which involves large quaternary and tertiary rearrangements. The mechanisms of the transmission of the regulatory(More)
The 2.54 A resolution structure of Ni-Fe hydrogenase has revealed the existence of hydrophobic channels connecting the molecular surface to the active site. A crystallographic analysis of xenon binding together with molecular dynamics simulations of xenon and H2 diffusion in the enzyme interior suggest that these channels serve as pathways for gas access to(More)
Aspartate transcarbamylase (ATCase) is a classic example of an allosteric enzyme. It catalyzes the conversion of aspartate to carbamyl aspartate, which is the first substrate in the biosynthesis of pyrimidines. Although ATCase is well characterized, both structurally and biochemically, little is known at the atomic level about the large amplitude motions(More)
The fluorescent protein KillerRed generates reactive oxygen species through the CALI effect. This property paves the way for the design of genetically encoded photosensitizers for use in cell killing and cancer photodynamic therapy. In this article, we have investigated the diffusion pathways of di-oxygen and the superoxide radical in KillerRed, using(More)
Photoactivatable fluorescent proteins (FPs) are powerful fluorescent highlighters in live cell imaging and offer perspectives for optical nanoscopy and the development of biophotonic devices. Two types of photoactivation are currently being distinguished, reversible photoswitching between fluorescent and nonfluorescent forms and irreversible(More)
Aspartate transcarbamylase (ATCase) is an important control enzyme in the pyrimidine biosynthetic pathway in Escherichia coli. It is a classic example of an allosteric protein and has been extensively studied biochemically, kinetically and structurally. As yet, however, a detailed model for the cooperative transition between the tensed (T) and relaxed (R)(More)
The glycine decarboxylase complex consists of four different proteins (the L-, P-, H-, and T-proteins). The H-protein plays a central role in communication among the other enzymes, as its lipoamide arm interacts successively with each of the components of the complex. The crystal structures of two states of the H-protein have been resolved: the oxidized(More)
The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H(2)O(2) -->1/2 O(2) + H(2)O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary(More)