Accurate three states model for amino acids with two chemically coupled titrating sites in explicit solvent atomistic constant pH simulations and pK_a calculations.

Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a “water” molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing “water” molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH

Arginine52 controls the photoisomerization process in photoactive yellow protein

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Increased primary health care use in the fi rst year after colorectal cancer diagnosis

Abstract Objective. The view that the general practitioner (GP) should be more involved during the curative treatment of cancer is gaining support. This study aimed to assess the current role of the GP during treatment of patients with colorectal cancer (CRC). Design. Historical prospective study, using primary care data from two cohorts. Setting. Registration Network Groningen (RNG) consisting of 18 GPs in three group practices with a dynamic population of about 30 000 patients. Subjects. Patients who underwent curative treatment for CRC (n ϭ 124) and matched primary care patients without CRC (reference population; n ϭ 358). Main outcome measures. Primary healthcare use in the period 1998 -2009. Findings . Patients with CRC had higher primary healthcare use in the year after diagnosis compared with the reference population. After correction for age, gender, and consultation behaviour, CRC patients had 54% (range 23 -92%) more face-to-face contacts, 68% (range 36 -108%) more drug prescriptions, and 35% (range -4 -90%) more referrals compared with reference patients. Patients consulted their GP more often for reasons related to anaemia, abdominal pain, constipation, skin problems, and urinary infections. GPs also prescribed more acid refl ux drugs, laxatives, anti-anaemic preparations, analgesics, and psycholeptics for CRC patients. Conclusions. The GP plays a signifi cant role in the year after CRC diagnosis. This role may be associated with treatment-related side effects and psychological problems. Formal guidelines on the involvement of the GP during CRC treatment might ensure more effective allocation and communication of care between primary and secondary healthcare services

Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study

Cytochrome P450 2D6 (CYP2D6) is one of the most important cytochromes P450 in humans. Resonance Raman data from the T309V mutant of CYP2D6 show that the substitution of the conserved I-helix threonine situated in the enzyme’s active site perturbs the heme spin equilibrium in favor of the six-coordinated low-spin species. A mechanistic hypothesis is introduced to explain the experimental observations, and its compatibility with the available structural and spectroscopic data is tested using quantum-mechanical density functional theory calculations on active-site models for both the CYP2D6 wild type and the T309V mutant