Search

Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (C c O) is still an open problem. The propionic acids of heme a 3 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 C c O 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 CH 2 twisting modes of the propionates to the protonation state of the individual heme a and heme a 3 propionates respectively. The comparison between calculated and measured H 2 O D 2 O 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 a 3 only protonation of one heme a 3 propionates was observed. Our data supports the postulated scenario where the heme a 3 propionates are involved in the proton pathway. [ABSTRACT FROM AUTHOR]

The metabolism of aerobic life uses the conversion of molecular oxygen to water as an energy source. This reaction is catalyzed by cytochrome c oxidase (C c O) consuming four electrons and four protons, which move along specific routes. While all four electrons are transferred via the same cofactors to the binuclear reaction center (BNC), the protons take two different routes in the A-type C c O, i.e., two of the four chemical protons consumed in the reaction arrive via the D-channel in the oxidative first half starting after oxygen binding. The other two chemical protons enter via the K-channel in the reductive second half of the reaction cycle. To date, the mechanism behind these separate proton transport pathways has not been understood. In this study, we propose a model that can explain the reaction-step specific opening and closing of the K-channel by conformational and p K A changes of its central lysine 362. Molecular dynamics simulations reveal an upward movement of Lys362 towards the BNC, which had already been supposed by several experimental studies. Redox state-dependent p K A calculations provide evidence that Lys362 may protonate transiently, thereby opening the K-channel only in the reductive second half of the reaction cycle. From our results, we develop a model that assigns a key role to Lys362 in the proton gating between the two proton input channels of the A-type C c O. [ABSTRACT FROM AUTHOR]

Higherorganisms defend themselves against invading micro-organisms and harmfulsubstances with their immune system. Key players of the immune systemare the white blood cells (WBC), which in case of infection move inan extravasation process from blood vessels toward infected tissuepromoting inflammation. This process starts with the attachment ofthe WBC to the blood vessel wall, mediated by protein pair interactionsof selectins and counter-receptors (C-R). Individual selectin C-Rbinding is weak and varies only moderately between the three selectintypes. Multivalency enhances such small differences, rendering selectin-bindingtype specific. In this work, we study selectin C-R binding, the initialstep of extravasation. We performed electrostatic energy computationsbased on the crystal structure of one selectin type co-crystallizedwith the ligating part of the C-R. The agreement with measured freeenergies of binding is satisfactory. Additionally, we modeled selectinmutant structures in order to explain differences in binding of thedifferent selectin types. To verify our modeling procedures, surfaceplasmon resonance data were measured for several mutants and comparedwith computed binding affinities. Binding affinities computed withsoaked rather than co-crystallized selectin C-R structures do notagree with measured data. Hence, these structures are inappropriateto describe the binding mode. The analysis of selectin/C-R bindingunravels the role played by individual molecular components in thebinding event. This opens new avenues to prevent immune system malfunction,designing drugs that can control inflammatory processes by moderatingselectin C-R binding. [ABSTRACT FROM AUTHOR]

Cytochrome coxidase (CcO) isa central enzyme in aerobic life catalyzing the conversion of molecularoxygen to water and utilizing the chemical energy to pump protonsand establish an electrochemical gradient. Despite intense research,it is not understood how CcO achieves unidirectionalproton transport and avoids short circuiting the proton pump. Withinthis work, we analyzed the potential role of Glu286 as a proton valve.We performed unconstrained MD simulations of CcOwith an explicit membrane for up to 80 ns. Those MD simulations revealedthat deprotonated Glu286 (Glu286-) is repelled by the negatively chargedpropionic acid PRD of heme a3. Thus, it destabilizes apotential linear chain of waters in the hydrophobic cavity connectingGlu286 with PRD and the binuclear center (BNC). Conversely, protonatedGlu286 (Glu286H) may remain in an upward position (oriented towardPRD) and can stabilize the connecting linear water chain in the hydrophobiccavity. We calculated the pKaof Glu286under physiological conditions to be above 12, but this value decreasesto about 9 under increased water accessibility of Glu286. The lattervalue is in accordance with experimental measurements. In the timecourse of MD simulation, we also observed conformations where Glu286bridges between water molecules located on both sides (the D channelbeing connected to the N side and the hydrophobic cavity), which mightlead to proton backflow. [ABSTRACT FROM AUTHOR]

Background: Despite progress in conventional cancer therapies, cancer is still one of the leading causes of death in industrial nations. Therefore, an urgent need of progress in fighting cancer remains. A promising alternative to conventional methods is immune therapy. This relies on the fact that low-immunogenic tumours can be eradicated if an immune response against them is induced. Peptide vaccination is carried out by injecting tumour peptides into a patient to trigger a specific immune response against the tumour in its entirety. However, peptide vaccination is a highly complicated treatment and currently many factors like the optimal number of epitopes are not known precisely. Therefore, it is necessary to evaluate how certain parameters influence the therapy. Results: We present the VaccImm Server that allows users to simulate peptide vaccination in cancer therapy. It uses an agent-based model that simulates peptide vaccination by explicitly modelling the involved cells (immune system and cancer) as well as molecules (antibodies, antigens and semiochemicals). As a new feature, our model uses real amino acid sequences to represent molecular binding sites of relevant immune cells. The model is used to generate detailed statistics of the population sizes and states of the single cell types over time. This makes the VaccImm web server well suited to examine the parameter space of peptide vaccination in silico. VaccImm is publicly available without registration on the web at http://bioinformatics.charite.de/vaccimm; all major browsers are supported. Conclusions: The VaccImm Server provides a convenient way to analyze properties of peptide vaccination in cancer therapy. Using the server, we could gain interesting insights into peptide vaccination that reveal the complex and patient-specific nature of peptide vaccination. [ABSTRACT FROM AUTHOR]

Peptide vaccination in cancer therapy is a promising alternative to conventional methods. However, the parameters for this personalized treatment are difficult to access experimentally. In this respect, in silico models can help to narrow down the parameter space or to explain certain phenomena at a systems level. Herein, we develop two empirical interaction potentials specific to B-cell and T-cell receptor complexes and validate their applicability in comparison to a more general potential. The interaction potentials are applied to the model VaccImm which simulates the immune response against solid tumors under peptide vaccination therapy. This multi-agent system is derived from another immune system simulator (CImmSim) and now includes a module that enables the amino acid sequence of immune receptors and their ligands to be taken into account. The multi-agent approach is combined with approved methods for prediction of major histocompatibility complex (MHC)-binding peptides and the newly developed interaction potentials. In the analysis, we critically assess the impact of the different modules on the simulation with VaccImm and how they influence each other. In addition, we explore the reasons for failures in inducing an immune response by examining the activation states of the immune cell populations in detail. In summary, the present work introduces immune-specific interaction potentials and their application to the agent-based model VaccImm which simulates peptide vaccination in cancer therapy. [ABSTRACT FROM AUTHOR]

Currently, cancer is one of the leading causes of death in industrial nations. While conventional cancer treatment usually results in the patient suffering from severe side effects, immunotherapy is a promising alternative. Nevertheless, some questions remain unanswered with regard to using immunotherapy to treat cancer hindering it from being widely established. To help rectify this deficit in knowledge, experimental data, accumulated from a huge number of different studies, can be integrated into theoretical models of the tumor-immune system interaction. Many complex mechanisms in immunology and oncology cannot be measured in experiments, but can be analyzed by mathematical simulations. Using theoretical modeling techniques, general principles of tumor-immune system interactions can be explored and clinical treatment schedules optimized to lower both tumor burden and side effects. In this paper, we aim to explain the main mathematical and computational modeling techniques used in tumor immunology to experimental researchers and clinicians. In addition, we review relevant published work and provide an overview of its impact to the field. [ABSTRACT FROM AUTHOR]

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 N ε. However, a neutral H250 with a proton at N ε 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. [ABSTRACT FROM AUTHOR]