Shared decision-making in routine breast cancer care in Germany-A cross-sectional study.

OBJECTIVE: Many preference-sensitive decisions have to be made in breast cancer care and little is known about the decision-making processes between breast cancer patients and the different health care professionals engaged in their treatment. METHODS: All female breast cancer patients who underwent surgery in four German breast centers between 07/2016 and 12/2018 were invited to fill in a survey. The decision-making process was evaluated using the 9-item Shared Decision Making Questionnaire (SDM-Q-9) and a German measure to assess satisfaction with care (ZAPA). The higher the total score (0-100), the higher the experienced degree of participation and satisfaction, respectively. Participants were asked to separately rate consultations with their inpatient hospital doctors, outpatient gynecologists, outpatient oncologists and primary care providers. An overall mean score for the degree of participation and the satisfaction with care was calculated for each patient across all consultations assessed. Differences between the 4 treating physician groups were analyzed as well. RESULTS: Of 1068 approached patients, 563 with a mean age of 62 and a standard deviation (SD) of 12.2 years filled in the survey (response rate: 53%). The overall SDM-Q-9 score was 73.8 (SD: 20.8). Older patients stated a higher level of participation than younger, different physician groups were rated quite similarly. Overall satisfaction with care was 87.4 (SD: 15.5). CONCLUSIONS: Overall, patients reported to have experienced a high level of shared decision-making (SDM) and were quite satisfied with their treatment. However, we do not know whether non-responders might have had different experiences.

Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates.

Cytochrome c oxidase (CcO) pumps protons from the N-side to the P-side and consumes electrons from the P-side of the mitochondrial membrane driven by energy gained from reduction of dioxygen to water. ATP synthesis uses the resulting proton gradient and electrostatic potential difference. Since the distance a proton travels through CcO is too large for a one-step transfer process, proton-loading sites (PLS) that can carry protons transiently are necessary. One specific pump-active PLS couples to the redox reaction, thus energizing the proton to move across the membrane against electric potential and proton gradient. The PLS should also prevent proton backflow. Therefore, the propionates of the two redox-active hemes in CcO were suggested as PLS candidates although, according to CcO crystal structures, none of the four propionates can be protonated on account of strong H-bonds. Here, we show that modeling the local structure around heme a3 propionates enhances significantly their capability of carrying a proton jointly. This was not possible for the propionates of heme a. The modeled structures are stable in molecular dynamics simulations (MDS) and are energetically similar to the crystal structure. Precise electrostatic energy computations of MDS data are used to estimate the pKA values of all titratable residues in CcO. For the modeled structures, the heme a3 propionates have pKA values high enough to host a proton transiently but not too high to fix the proton permanently. The change in pKA throughout the redox reaction is sufficient to push the proton to the P-side of the membrane and to provide the protons with the necessary amount of energy for ATP synthesis.

Quantification of Local Electric Field Changes at the Active Site of Cytochrome c Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations.

Cytochrome c oxidase (CcO) is a transmembrane protein complex that reduces molecular oxygen to water while translocating protons across the mitochondrial membrane. Changes in the redox states of its cofactors trigger both O2 reduction and vectorial proton transfer, which includes a proton-loading site, yet unidentified. In this work, we exploited carbon monoxide (CO) as a vibrational Stark effect (VSE) probe at the binuclear center of CcO from Rhodobacter sphaeroides. The CO stretching frequency was monitored as a function of the electrical potential, using Fourier transform infrared (FTIR) absorption spectroelectrochemistry. We observed three different redox states (R4CO, R2CO, and O), determined their midpoint potential, and compared the resulting electric field to electrostatic calculations. A change in the local electric field strength of +2.9 MV/cm was derived, which was induced by the redox transition from R4CO to R2CO. We performed potential jump experiments to accumulate the R2CO and R4CO species and studied the FTIR difference spectra in the protein fingerprint region. The comparison of the experimental and computational results reveals that the key glutamic acid residue E286 is protonated in the observed states, and that its hydrogen-bonding environment is disturbed upon the redox transition of heme a3. Our experiments also suggest propionate A of heme a3 changing its protonation state in concert with the redox state of a second cofactor, heme a. This supports the role of propionic acid side chains as part of the proton-loading site.

Empirical Conversion of pK a Values between Different Solvents and Interpretation of the Parameters: Application to Water, Acetonitrile, Dimethyl Sulfoxide, and Methanol.

An empirical conversion method (ECM) that transforms pK a values of arbitrary organic compounds from one solvent to the other is introduced. We demonstrate the method's usefulness and performance on pK a conversions involving water and organic solvents acetonitrile (MeCN), dimethyl sulfoxide (Me2SO), and methanol (MeOH). We focus on the pK a conversion from the known reference value in water to the other three organic solvents, although such a conversion can also be performed between any pair of the considered solvents. The ECM works with an additive parameter that is specific to a solvent and a molecular family (essentially characterized by a functional group that is titrated). We formally show that the method can be formulated with a single additive parameter, and that the extra multiplicative parameter used in other works is not required. The values of the additive parameter are determined from known pK a data, and their interpretation is provided on the basis of physicochemical concepts. The data set of known pK a values is augmented with pK a values computed with the recently introduced electrostatic transform method, whose validity is demonstrated. For a validation of our method, we consider pK a conversions for two data sets of titratable compounds. The first data set involves 81 relatively small molecules belonging to 19 different molecular families, with the pK a data available in all four considered solvents. The second data set involves 76 titratable molecules from 5 additional molecular families. These molecules are typically larger, and their experimental pK a values are available only in Me2SO and water. The validation tests show that the agreement between the experimental pK a data and the ECM predictions is generally good, with absolute errors often on the order of 0.5 pH units. The presence of a few outliers is rationalized, and observed trends with respect to molecular families are discussed.

Retraction: The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation.

Retraction of 'The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation' by Hendrik Mohrmann et al., Phys. Chem. Chem. Phys., 2017, DOI: .

The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation.

Cytochrome c oxidase (CcO) is a membrane protein of the respiratory chain that catalytically reduces molecular oxygen (O2) to water while translocating protons across the membrane. The enzyme hosts two copper and two heme iron moieties (heme a/heme a3). The atomic details of the sequential steps that go along with this redox-driven proton translocation are a matter of debate. Particularly for the reductive phase of CcO that precedes oxygen binding experimental data are scarce. Here, we use CcO under anaerobic conditions where carbon monoxide (CO) is bound to heme a3 which in tandem with CuB forms the binuclear center (BNC). Fourier-transform infrared (FTIR) absorption spectroscopy is combined with electro-chemistry to probe different redox and protonation states populated by variation of the external electrostatic potential. With this approach, the redox behavior of heme a and the BNC could be separated and the corresponding redox potentials were determined. We also infer the protonation of one of the propionate side chains of heme a3 to correlate with the oxidation of heme a. Experimental changes in the local electric field surrounding CO bound to heme a3 are determined by their vibrational Stark effect and agree well with electrostatic computations. The comparison of experimental and computational results indicates that changes of the heme a3/CuB redox state are coupled to proton transfer towards heme a3. The latter supports the role of the heme a3 propionate D as proton loading site.

Protonation-State-Dependent Communication in Cytochrome c Oxidase.

Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both a redox enzyme and a proton pump, proton transfer into the protein toward the BNC or toward a proton loading site (and ultimately through the membrane) must be highly regulated. The PR → F transition is the first step in a catalytic cycle that requires proton transfer from the bulk at the N-side to the BNC. Molecular dynamics simulations of the PR → F intermediate of this transition, with 16 different combinations of protonation states of key residues in the D- and K-channel, show the impact of the K-channel on the D-channel to be protonation-state dependent. Strength as well as means of communication, correlations in positions, or communication along the hydrogen-bonded network depends on the protonation state of the K-channel residue K362. The conformational and hydrogen-bond dynamics of the D-channel residue N139 is regulated by an interplay of protonation in the D-channel and K362. N139 thus assumes a gating function by which proton passage through the D-channel toward E286 is likely facilitated for states with protonated K362 and unprotonated E286. In contrast, proton passage through the D-channel is hindered by N139's preference for a closed conformation in situations with protonated E286.

Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome.

Photoisomerization of a protein-bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine bridge between rings C and D. Ground-state heterogeneity of the chromophore has been reported for both Pr and Pfr. Here, we report ultrafast visible (Vis) pump-probe and femtosecond polarization-resolved Vis pump-infrared (IR) probe studies of the Pfr photoreaction in native and 13 C/15 N-labeled Cph1 phytochrome with unlabeled PCB chromophore, demonstrating different S0 substates, Pfr-I and Pfr-II, with distinct IR absorptions, orientations and dynamics of the carbonyl vibration of ring D. We derived time constants of 0.24 ps, 0.7 ps and 6 ps, describing the complete initial photoreaction. We identified an isomerizing pathway with 0.7 ps for Pfr-I, and silent dynamics with 6 ps for Pfr-II. We discuss different origins of the Pfr substates, and favor different facial orientations of ring D. The model provides a quantum yield for Pfr-I of 38%, in line with ~35% ring D rotation in the electronic excited state. We tentatively assign the silent form Pfr-II to a dark-adapted state that can convert to Pfr-I upon light absorption.

Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1.

Agp1 is a prototypical bacterial phytochrome from Agrobacterium fabrum harboring a biliverdin cofactor which reversibly photoconverts between a red-light-absorbing (Pr) and a far-red-light-absorbing (Pfr) states. The reaction mechanism involves the isomerization of the bilin-chromophore followed by large structural changes of the protein matrix that are coupled to protonation dynamics at the chromophore binding site. Histidines His250 and His280 participate in this process. Although the three-dimensional structure of Agp1 has been solved at high resolution, the precise position of hydrogen atoms and protonation pattern in the chromophore binding pocket has not been investigated yet. Here, we present protonated structure models of Agp1 in the Pr state involving appropriately placed hydrogen atoms that were generated by hybrid quantum mechanics/molecular mechanics- and electrostatic calculations and validated against experimental structural- and spectroscopic data. Although the effect of histidine protonation on the vibrational spectra is weak, our results favor charge neutral H250 and H280 both protonated at Nε. However, a neutral H250 with a proton at Nε and a cationic H280 may also be possible. Furthermore, the present QM/MM calculations of IR and Raman spectra of Agp1 containing isotope-labeled BV provide a detailed vibrational assignment of the biliverdin modes in the fingerprint region.

Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations.

Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme a3 have been proposed to act as a proton loading site (PLS) in the proton pumping pathway, yet this proposal could not be verified by experimental data so far. We have set up an experiment where the redox states of the two hemes in CcO can be controlled via external electrical potential. Surface enhanced resonance Raman (SERR) spectroscopy was applied to simultaneously monitor the redox state of the hemes and the protonation state of the heme propionates. Simulated spectra based on QM/MM calculations were used to assign the resonant enhanced CH2 twisting modes of the propionates to the protonation state of the individual heme a and heme a3 propionates respectively. The comparison between calculated and measured H2OD2O difference spectra allowed a sound band assignment. In the fully reduced enzyme at least three of the four heme propionates were found to be protonated whereas in the presence of a reduced heme a and an oxidized heme a3 only protonation of one heme a3 propionates was observed. Our data supports the postulated scenario where the heme a3 propionates are involved in the proton pathway.

Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII.

Structural data of the oxygen-evolving complex (OEC) in photosystem II (PSII) determined by X-ray crystallography, quantum chemistry (QC), and extended X-ray absorption fine structure (EXAFS) analyses are presently inconsistent. Therefore, a detailed study of what information can be gained about the OEC through a comparison of QC and crystallographic structure information combined with the information from range-extended EXAFS spectra was undertaken. An analysis for determining the precision of the atomic coordinates of the OEC by QC is carried out. OEC model structures based on crystallographic data that are obtained by QC from different research groups are compared with one another and with structures obtained by high-resolution crystallography. The theory of EXAFS spectra is summarized, and the application of EXAFS spectra to the experimental determination of the structure of the OEC is detailed. We discriminate three types of parameters entering the formula for the EXAFS spectrum: (1) model-independent, predefined, and fixed; (2) model-dependent that can be computed or adjusted; and (3) model-dependent that must be adjusted. The information content of EXAFS spectra is estimated and is related to the precision of atomic coordinates and resolution power to discriminate different atom-pair distances of the OEC. It is demonstrated how a precise adjustment of atomic coordinates can yield a nearly perfect representation of the experimental OEC EXAFS spectrum, but at the expense of overfitting and losing the knowledge of the initial OEC model structure. Introducing a novel type of penalty function, it is shown that moderate adjustment of atomic coordinates to the EXAFS spectrum limited by constraints avoids overfitting and can be used to validate different OEC model structures. This technique is used to identify the OEC model structures whose computed OEC EXAFS spectra agree best with the measured spectrum. In this way, the most likely S-state and protonation pattern of the OEC for the most recent high-resolution crystal structure of PSII are determined. We find that the X-ray free-electron laser (XFEL) structure is indeed not significantly affected by exposure to XFEL pulses and thus results in a radiation-damage-free model of the OEC.

RETRACTED: Protonation State-Dependent Communication in Cytochrome c Oxidase.

Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both redox enzyme and proton pump, proton transfer out of either of the channels toward the BNC or into the protein toward a proton loading site, and ultimately through the membrane, must be highly regulated. The O→E intermediate of cytochrome c oxidase is the first redox state in its catalytic cycle, where proton transfer through the K-channel, from K362 to Y288 at the BNC, is important. Molecular dynamics simulations of this intermediate with 16 different combinations of protonation states of key residues in the D- and K-channel show the mutual impact of the two proton-conducting channels to be protonation state-dependent. Strength as well as means of communication, correlations in positions, or connections along the hydrogen-bonded network, change with the protonation state of the K-channel residue K362. The conformational and hydrogen-bond dynamics of the D-channel residue N139 regulated by an interplay of protonation in the D-channel and K362. N139 thus assumes a gating function by which proton passage through the D-channel toward E286 is likely facilitated for states with protonated K362 and unprotonated E286, which would in principle allow proton transfer to the BNC, but no proton pumping until a proton has reached E286.

Computing pKa Values in Different Solvents by Electrostatic Transformation.

We introduce a method that requires only moderate computational effort to compute pKa values of small molecules in different solvents with an average accuracy of better than 0.7 pH units. With a known pKa value in one solvent, the electrostatic transform method computes the pKa value in any other solvent if the proton solvation energy is known in both considered solvents. To apply the electrostatic transform method to a molecule, the electrostatic solvation energies of the protonated and deprotonated molecular species are computed in the two considered solvents using a dielectric continuum to describe the solvent. This is demonstrated for 30 molecules belonging to 10 different molecular families by considering 77 measured pKa values in 4 different solvents: water, acetonitrile, dimethyl sulfoxide, and methanol. The electrostatic transform method can be applied to any other solvent if the proton solvation energy is known. It is exclusively based on physicochemical principles, not using any empirical fetch factors or explicit solvent molecules, to obtain agreement with measured pKa values and is therefore ready to be generalized to other solute molecules and solvents. From the computed pKa values, we obtained relative proton solvation energies, which agree very well with the proton solvation energies computed recently by ab initio methods, and used these energies in the present study.

Proton solvation in protic and aprotic solvents.

Protonation pattern strongly affects the properties of molecular systems. To determine protonation equilibria, proton solvation free energy, which is a central quantity in solution chemistry, needs to be known. In this study, proton affinities (PAs), electrostatic energies of solvation, and pKA values were computed in protic and aprotic solvents. The proton solvation energy in acetonitrile (MeCN), methanol (MeOH), water, and dimethyl sulfoxide (DMSO) was determined from computed and measured pKA values for a specially selected set of organic compounds. pKA values were computed with high accuracy using a combination of quantum chemical and electrostatic approaches. Quantum chemical density functional theory computations were performed evaluating PA in the gas-phase. The electrostatic contributions of solvation were computed solving the Poisson equation. The computations yield proton solvation free energies with high accuracy, which are in MeCN, MeOH, water, and DMSO -255.1, -265.9, -266.3, and -266.4 kcal/mol, respectively, where the value for water is close to the consensus value of -265.9 kcal/mol. The pKA values of MeCN, MeOH, and DMSO in water correlates well with the corresponding proton solvation energies in these liquids, indicating that the solvated proton was attached to a single solvent molecule.

pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories.

For a benchmark set of 194 measured pKa values in 13 proteins, electrostatic energy computations are performed in which pKa values are computed by solving the Poisson-Boltzmann equation. In contrast to the previous approach of Karlsberg(+) (KB(+)) that essentially used protein crystal structures with variations in their side chain conformations, the present approach (KB2(+)MD) uses protein conformations from four molecular dynamics (MD) simulations of 10 ns each. These MD simulations are performed with different specific but fixed protonation patterns, selected to sample the conformational space for the different protonation patterns faithfully. The root-mean-square deviation between computed and measured pKa values (pKa RMSD) is shown to be reduced from 1.17 pH units using KB(+) to 0.96 pH units using KB2(+)MD. The pKa RMSD can be further reduced to 0.79 pH units, if each conformation is energy-minimized with a dielectric constant of εmin = 4 prior to calculating the electrostatic energy. The electrostatic energy expressions upon which the computations are based have been reformulated such that they do not involve terms that mix protein and solvent environment contributions and no thermodynamic cycle is needed. As a consequence, conformations of the titratable residues can be treated independently in the protein and solvent environments. In addition, the energy terms used here avoid the so-called intrinsic pKa and can therefore be interpreted without reference to arbitrary protonation states and conformations.

pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements.

Knowledge on pK(A) values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson-Boltzmann equation (lPBE) can successfully be used to compute pK(A) values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK(A) values. This work focuses on a comparison between pK(A) computations obtained with the well-established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK(A) values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK(A) values and we show for the FE method how different parameters influence the accuracy of computed pK(A) values.

ProPairs: A Data Set for Protein-Protein Docking.

ProPairs is a data set of crystal structures of protein complexes defined as biological assemblies in the protein data bank (PDB), which are classified as legitimate protein-protein docking complexes by also identifying the corresponding unbound protein structures in the PDB. The underlying program selecting suitable protein complexes, also called ProPairs, is an automated method to extract structures of legitimate protein docking complexes and their unbound partner proteins from the PDB which fulfill specific criteria. In this way a total of 5,642 protein complexes have been identified with 11,600 different decompositions in unbound protein pairs yielding legitimate protein docking partners. After removing sequence redundancy (requiring a sequence identity of the residues in the interface of less than 40%), 2,070 different legitimate protein docking complexes remain. For 810 of these protein docking complexes, both docking partners possess corresponding unbound structures in the PDB. From the 2,070 nonredundant protein docking complexes there are 417 which possess a cofactor at the interface. From the 176 protein docking complexes of the Protein-Protein Docking Benchmark 4.0 (DB4.0) data set, 13 differ from the ProPairs data set. Twelve of them differ with respect to the composition of the unbound structures but are contained in the large redundant ProPairs data set. One protein docking complex of the DB4.0 data set is not contained in ProPairs since the biological assembly specified in the PDB is wrong (PDB id 1d6r ). For one protein complex (PDB id 1bgx ) the DB4.0 data set uses a fabricated unbound structure. For public use interactive online access is provided to the ProPairs data set of nonredundant protein docking complexes along with the source code of the underlying method [ http://propairs.github.io].

Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.

The DOcking decoy-based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance-dependent atom-pair interactions. To optimize the atom-pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand-receptor systems (or just pairs). Thus, a total of 8609 ligand-receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand-receptor systems, 1000 evenly sampled docking decoys with 0-10 Å interface root-mean-square-deviation (iRMSD) were generated with a method used before for protein-protein docking. A neural network-based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel-like energy landscape for the interaction between these hypothetical ligand-receptor systems. Thus, our method hierarchically models the overall funnel-like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom-pair-based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation-dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand-receptor systems and their decoys are freely available at http://agknapp.chemie.fu-berlin.de/doop/.