A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics

NaWuReT Colloquium: From PhD Student to Assistant Professor – Early Career Chemical Engineers in Academia

The Nachwuchs Reaktionstechnik (NaWuReT) are early-career scientists from the ProcessNet Division Reaction Engineering. In autumn 2021, they organized an online colloquium with international early-career scientists from the chemical engineering community. Five guests were invited to give a scientific talk and provide insights into their career paths. The guests gave advice and emphasized the main challenges and opportunities during their early careers. Crucial points are networking, guidance, mentoring, as well as funding acquisition and the personal work-life balance

Accessing ns–μs side chain dynamics in ubiquitin with methyl RDCs

This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098–6107, 2001; Lakomek in J Biomol NMR 34:101–115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τc dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τc. In fact, the average amplitude of motion expressed in terms of order parameters S2 associated with the supra-τc window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959–8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471–1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains

Development and Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

Ristola M. on työryhmien DAD Study Grp ; Royal Free Hosp Clin Cohort ; INSIGHT Study Grp ; SMART Study Grp ; ESPRIT Study Grp jäsen.Background Chronic kidney disease (CKD) is a major health issue for HIV-positive individuals, associated with increased morbidity and mortality. Development and implementation of a risk score model for CKD would allow comparison of the risks and benefits of adding potentially nephrotoxic antiretrovirals to a treatment regimen and would identify those at greatest risk of CKD. The aims of this study were to develop a simple, externally validated, and widely applicable long-term risk score model for CKD in HIV-positive individuals that can guide decision making in clinical practice. Methods and Findings A total of 17,954 HIV-positive individuals from the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) study with >= 3 estimated glomerular filtration rate (eGFR) values after 1 January 2004 were included. Baseline was defined as the first eGFR > 60 ml/min/1.73 m2 after 1 January 2004; individuals with exposure to tenofovir, atazanavir, atazanavir/ritonavir, lopinavir/ritonavir, other boosted protease inhibitors before baseline were excluded. CKD was defined as confirmed (>3 mo apart) eGFR In the D:A:D study, 641 individuals developed CKD during 103,185 person-years of follow-up (PYFU; incidence 6.2/1,000 PYFU, 95% CI 5.7-6.7; median follow-up 6.1 y, range 0.3-9.1 y). Older age, intravenous drug use, hepatitis C coinfection, lower baseline eGFR, female gender, lower CD4 count nadir, hypertension, diabetes, and cardiovascular disease (CVD) predicted CKD. The adjusted incidence rate ratios of these nine categorical variables were scaled and summed to create the risk score. The median risk score at baseline was -2 (interquartile range -4 to 2). There was a 1: 393 chance of developing CKD in the next 5 y in the low risk group (risk score = 5, 505 events), respectively. Number needed to harm (NNTH) at 5 y when starting unboosted atazanavir or lopinavir/ritonavir among those with a low risk score was 1,702 (95% CI 1,166-3,367); NNTH was 202 (95% CI 159-278) and 21 (95% CI 19-23), respectively, for those with a medium and high risk score. NNTH was 739 (95% CI 506-1462), 88 (95% CI 69-121), and 9 (95% CI 8-10) for those with a low, medium, and high risk score, respectively, starting tenofovir, atazanavir/ritonavir, or another boosted protease inhibitor. The Royal Free Hospital Clinic Cohort included 2,548 individuals, of whom 94 individuals developed CKD (3.7%) during 18,376 PYFU (median follow-up 7.4 y, range 0.3-12.7 y). Of 2,013 individuals included from the SMART/ESPRIT control arms, 32 individuals developed CKD (1.6%) during 8,452 PYFU (median follow-up 4.1 y, range 0.6-8.1 y). External validation showed that the risk score predicted well in these cohorts. Limitations of this study included limited data on race and no information on proteinuria. Conclusions Both traditional and HIV-related risk factors were predictive of CKD. These factors were used to develop a risk score for CKD in HIV infection, externally validated, that has direct clinical relevance for patients and clinicians to weigh the benefits of certain antiretrovirals against the risk of CKD and to identify those at greatest risk of CKD.Peer reviewe

Charakterisierung eines instationären Reaktionssystems mittels Pulsreaktion am Beispiel der CO-Methanisierung

Gegenstand der Untersuchung ist die Nutzung von Pulsreaktionen zur Charakterisierung der Methanisierung von CO an geträgerten Nickel-Katalysatoren im instationären Zustand. Die Untersuchung erfolgt im Kontext der Power-to-Gas-Konzepte, welche im Rahmen der chemischen Speicherung elektrischer Energie diskutiert werden. Die CO-Methanisierung ist wissenschaftlich und technisch als etablierter Prozess zu bezeichnen. Die Kenntnisse der ablaufenden Vorgänge können durch gezielte Untersuchung für den instationären Zustand dieses Reaktionssystems jedoch weiter ausgebaut werden. In der vorliegenden Arbeit werden Pulsreaktionen als leicht umsetzbare Untersuchungsmethode vorgestellt. Anhand von drei Untersuchungsreihen werden Möglichkeiten der Charakterisierung aufgezeigt. Die Ergebnisse stellen die Bedeutung der in-situ bestimmten Adsorptionskapazität des Katalysators heraus, welche als wichtige Referenz in den Untersuchungen genutzt wird. In den ersten beiden Untersuchungsreihen wurden CO-Pulse in einen Trägergasstrom injiziert, welcher das zweite Edukt Wasserstoff H2 kontinuierlich und im Überschuss zur Verfügung stellte. Für einzelne Pulse wird die Momentenanalyse und für periodisch dosierte Pulse (Pulsserien), die transiente Materialbilanz als Auswertungsgrundlage genutzt. Aus der Analyse der Einzelpulse wird eine irreversible Bindung von CO an den Katalysator und deutliche Hinweise für die Hydrierung von adsorbierten Kohlenstoff als geschwindigkeitsbestimmenden Teilschritt festgestellt. Die Pulsserien vereinen Informationen aus zwei unterschiedlichen Untersuchungsmethoden, welche das instationäre Reaktionssystem mittels sprungförmiger und periodischer Konzentrationsänderungen analysieren. Die anhaltende pulsförmige Dosierung zeigt in der Untersuchungsreihe einen periodischen Grenzzyklus, welcher zwischen Einlauf- und Auslaufphase (Konzentrationssprünge) liegt. Die erhaltenen transienten Konzentrationsverläufe geben einen guten Einblick in die Wechselwirkungen im Reaktionssystem. Die Speicherung von Wasser im Trägermaterial des Katalysators, ebenso wie die Speicherung von teilhydrierten Kohlenstoffintermediaten, werden als wichtige Vorgänge für die instationären Abläufe in der CO-Methanisierung identifiziert. Auch wird die bedeckunsgradabhängige mittlere Reaktions-geschwindigkeit im Grenzzyklus durch ein kinetisches Modell approximiert. In der dritten Untersuchungsreihe wurden die Reaktanden nicht simultan, sondern konsekutiv eingesetzt. Die Untersuchung zeigt, dass eine Einspeicherung von CO in Inertgas, auch über längere Zeit, bei Reaktionstemperatur möglich ist. Es treten jedoch Nebenreaktionen auf, welche die Methanausbeute verringern und zu einer Einspeicherung von schlecht reaktivem Kohlenstoff führen. Gleichzeitig wird aber auch die Reversibilität der Einspeicherung festgestellt, welche vermutlich durch teilweise flüssige Nickelkristallite möglich gemacht wird. Die Ergebnisse der drei Untersuchungsreihen bestätigen und erweitern den Stand des Wissens für die instationäre CO-Methanisierung an Nickel-Trägerkatalysatoren. Die Erkenntnisse aus den ersten beiden Untersuchungsreihen kommen bei einer punktförmigen oder anhaltenden Überhöhung von CO bei ausreichender H2-Verfügbarkeit zum Tragen. Die Erkenntnisse der dritten Untersuchungsreihe geben Einblick in ein Betriebsszenario, in dem zu viel CO in das Reaktionssystem gelangt und H2 nicht ausreichend zur Verfügung steht und nachdosiert werden muss. Die Methode stellt nicht nur eine Vielzahl an Untersuchungsmöglichkeiten zur Verfügung, sondern erzielt übertragbare Ergebnisse, wie im Abgleich mit Literaturdaten gezeigt wird. Die Untersuchungsmethode zeichnet sich dadurch aus, dass sowohl Ergebnisse aus Modellexperimenten, als auch aus anwendungsnahen Untersuchungen im Zusammenhang analysiert werden können. Aus den Untersuchungsergebnissen können so Konsequenzen und Konzepte für den dynamischen Betrieb von Methanisierungsreaktoren abgeleitet werden.In this thesis pulse reactions are applied to characterise unsteady-state behaviour of carbon monoxide (CO) methanation catalysed by a supported nickel catalyst. Context of this study are power-to-gas-concepts, which are discussed in order to store excess electrical energy in chemicals. CO-methanation is a well-established technology form technical and scientific viewpoint. Nevertheless, knowledge can be expanded for ongoing processes in unsteady-state operation by focused investigation. Pulse reactions are presented and applied in this investigation as a feasible method of. Possibilities of characterisation are presented on the basis of three different experimental studies. Obtained experimental results show the importance of provided adsorption capacities by the catalyst, which are used as a primary reference in examination. In the first two studies CO pulses were injected in flowing carrier gas, which delivered the second reactant hydrogen (H2) continuously in excess. For single pulses, momentum analysis is applied, while for periodical injected pulses (pulse series) an analysis on basis of the transient mass balance is used. Single pulse experiments reveal an irreversible adsorption of CO on the catalyst and indicate, that carbon hydrogenation is the rate limiting step in CO methanation. Pulse series experiments combine information from two different methods, which analyse the unsteady-state behaviour of reaction systems by concentration step-response and forced periodical concentration. Continuous injection of pulses leads to a periodical limit cycle, which is located between a start-up and a relaxation period. Experimentally obtained transient concentration profiles give a good insight into interactions in the reaction system. Storage of water on the support material of the catalyst is detected, as well as partially hydrogenated carbon species on the catalyst surface. These processes are highly affecting unsteady-state behaviour in CO methanation. Furthermore a kinetic model is approximated for the periodical limit cycle by coverage depending reaction rate analysis. In a third study the reactants were dosed consecutively, so that they did not appear simultaneously in gas phase. The obtained results at reaction temperatures reveal a storage of CO on the catalyst in inert gas for a long time. However, side reactions are taking place, which reduce the methane yield and lead to formation of surface carbon with low reactivity. It is asserted, that formation of surface carbon is a reversible process, which is probably promoted by partly liquid nickel crystallites. The results of all three studies confirm and expand knowledge for CO methanation with supported nickel catalysts. Findings form the first two studies can be applied in cases of punctiform and ongoing fluctuation of CO in excess hydrogen. Findings from the third study give insight in operation modes, where H2 is not directly available and CO is entering the reaction system without the second reactant. The presented method can be applied in a wide variety as well as it shows transferrable results, which is shown by comparison with literature. The method is characterised by its ability to analyse model experiments as well as scenarios from technical applications. So it is possible to deduce concepts and consequences for dynamically operated methanation reactors

Study on the tolerance of low-temperature CO methanation with single pulse experiments

In this contribution, single pulse reaction experiments are discussed in the context of dynamic reactor operation and used to determine the tolerance of reactors arising from sorption effects at the catalyst surface. A defined amount of CO is dosed together with an internal standard (He) in a constant H2 stream, and the pulse response is observed with reference to the internal standard, which is representing the fluid dynamics of the injected pulse. Different responses are obtained depending on the catalyst mass (Ni/Al2O3) and the operation temperature (170°C-300°C). The tolerance of the reactor can be deduced from the experimental findings. On the one hand, the catalyst adsorption capacity determines the ability to buffer fluctuations at low reaction temperatures (<220 °), which are beneficial for full-conversion, overcoming thermodynamic restrictions. On the other hand, temperature determines the transient response of the system and is independent of the catalyst mass. From these findings the study reveals that reactors represent important buffer systems during load changes in dynamic operation modes and provide an intrinsic tolerance originating from sorption processes at the catalyst surface

The Periodic Transient Kinetics Method for Investigation of Kinetic Process Dynamics Under Realistic Conditions: Methanation as an Example

Due to rising interest for the integration of chemical energy storage into the electrical power grid, the unsteady-state operation of chemical reactors is gaining more and more attention with emphasis on heterogeneously catalyzed reactions. The transient response of those reactions is influenced by effects on different length scales, ranging from the active surface via the individual porous catalyst particle up to the full-scale reactor. The challenge, however, is to characterize unsteady-state effects under realistic operation conditions and to assign them to distinct transport processes. Therefore, the periodic transient kinetics (PTK) method is introduced, which allows for the separation of kinetic process dynamics at different length scales experimentally under realistic operation conditions. The methodology also provides the capability for statistical analysis of the experimental results and therefore improved reliability of the derived conclusions. Therefore, the PTK method provides the experimental basis for model-based derivation of reaction kinetics valid under dynamic conditions. The applicability of the methodology is demonstrated for the methanation reaction chosen as an example process for heterogeneously catalyzed reactions relevant for chemical energy storage purposes. <br /

Frequency Response Analysis of the Unsteady-State CO/CO2 Methanation Reaction: An Experimental Study

The utilization of renewable electricity for power-to-gas (PtG) applications induces fluctuations in the H2 availability from water electrolysis. For subsequent methanation of CO or CO2 the unsteady-state operation of the respective reactor allows to minimize H2 storage capacities. However, the impact of temporal fluctuations in feed gas composition on the methanation reaction and the respective transient kinetics has not yet been fully understood. We investigated the methanation of various CO/CO2 (COx) feed gas mixtures under periodically changing gas compositions with emphasis on the effect of the frequency on the reactor response. We show that the frequency response of CH4 exhibits a characteristic hysteresis, which depends on the switching direction between COx-lean and COx-rich feeds and their composition. From the shape of the hysteresis we are able to conclude on the preferred COx species being hydrogenated to CH4 under respective conditions, which also provides mechanistic insights. By applying high cycling frequencies, the highly reactive species present under CO methanation conditions can even selectively be activated, which explains the higher reactivity compared to steady-state conditions reported, frequently

Methanation of CO/CO2 mixtures: Evaluation of pellet size effect on methane formation rate and reactant selectivity

In the present contribution, numerical experiments are used to interpret results obtained from physical diffusion-influenced experiments for the CO and CO2 co-methanation. Physical and numerical experiments are conducted in the temperature range from 513 to 573 K and different CO/CO2 ratios. It is revealed that CO and CO2 behave very differently when both are simultaneously converted into CH4, which is mainly due to the competing reaction kinetics. Since CO inhibits the methanation of both CO2 and itself, large pellets and the associated diffusion limitation can be used to reduce the concentration of CO inside the pellets and hence its overall inhibiting effect. This catalyst design aspect can be used to increase the effective methane formation rate up to 35 % for a co-methanation of CO and CO2, while larger pellets allow to reduce the pressure drop in the reactor at the same time, which provides further advantages for reactor operation. Moreover, it is found that a selective CO methanation can be conducted with low-loading (nickel) catalysts, as long as the catalyst is operated in the low-temperature region (T << 300 °C) with small particle sizes below 1.5 mm. In addition, it is shown that industrially relevant catalysts significantly affect the reactant selectivity