Conformational selection in protein binding and function

Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select' protein conformations for binding (or unbinding). In this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in different conformations, which is plausible for small ligand molecules. Such a separation of timescales leads to a decoupling and temporal ordering of binding/unbinding events and conformational changes. We propose that conformational-selection and induced-change processes (such as induced fit) are two sides of the same coin, because the temporal ordering is reversed in binding and unbinding direction. Conformational-selection processes can be characterized by a conformational excitation that occurs prior to a binding or unbinding event, while induced-change processes exhibit a characteristic conformational relaxation that occurs after a binding or unbinding event. We discuss how the ordering of events can be determined from relaxation rates and effective on- and off-rates determined in mixing experiments, and from the conformational exchange rates measured in advanced NMR or single-molecule FRET experiments. For larger ligand molecules such as peptides, conformational changes and binding events can be intricately coupled and exhibit aspects of conformational-selection and induced-change processes in both binding and unbinding direction.Comment: review article; 10 pages, 4 figures, Protein Sci. 201

Urban Dust Microbiome: Impact on Later Atopy and Wheezing

INTRODUCTION: Investigations in urban areas have just begun to explore how the indoor dust microbiome may affect the pathogenesis of asthma and allery. We aimed to investigate the early fungal and bacterial microbiome in house dust with allergic sensitization and wheezing later in childhood. METHODS: Individual dust samples from 189 homes of the LISAplus birth cohort study were collected shortly after birth from living room floors and profiled for fungal and bacterial microbiome. Fungal and bacterial diversity was assessed with terminal restriction fragment length polymorphism (tRFLP) and defined by the Simpson diversity index. Information on wheezing outcomes and co-variates until the age of 10 years was obtained by parental questionnaires. Information on specific allergic sensitization was available at 6 and 10 years. Logistic regression and General Estimation Equation (GEE) models were used to examine the relationship between microbial diversity and health outcomes. RESULTS: Logistic regression analyses revealed a significantly reduced risk of developing sensitization to aero-allergens at 6 years and ever wheezing until the age of 10 years for exposure to higher fungal diversity (adjusted Odds Ratio aOR (95%CI): 0.26 (0.10-0.70)), and 0.42 (0.18-0.96), respectively), in adjusted analyses. The associations were attenuated for the longitudinal analyses (GEE) until the age of 10 years. There was no association between higher exposure to bacterial diversity and the tested health outcomes. CONCLUSION: Higher early exposure to fungal diversity might help to prevent from developing sensitization to aero-allergens in early childhood, but the reasons for attenuated effects in later childhood require further prospective studies

Carbon allocation to root exudates is maintained in mature temperate tree species under drought

- Carbon (C) exuded via roots is proposed to increase under drought and facilitate important ecosystem functions. However, it is unknown how exudate quantities relate to the total C budget of a drought-stressed tree, that is, how much of net-C assimilation is allocated to exudation at the tree level. - We calculated the proportion of daily C assimilation allocated to root exudation during early summer by collecting root exudates from mature Fagus sylvatica and Picea abies exposed to experimental drought, and combining above- and belowground C fluxes with leaf, stem and fine-root surface area. - Exudation from individual roots increased exponentially with decreasing soil moisture, with the highest increase at the wilting point. Despite c. 50% reduced C assimilation under drought, exudation from fine-root systems was maintained and trees exuded 1.0% (F. sylvatica) to 2.5% (P. abies) of net C into the rhizosphere, increasing the proportion of C allocation to exudates two- to three-fold. Water-limited P. abies released two-thirds of its exudate C into the surface soil, whereas in droughted F. sylvatica it was only one-third. - Across the entire root system, droughted trees maintained exudation similar to controls, suggesting drought-imposed belowground C investment, which could be beneficial for ecosystem resilience

High resilience of carbon transport in long-term drought-stressed mature Norway spruce trees within 2 weeks after drought release

Under ongoing global climate change, drought periods are predicted to increase in frequency and intensity in the future. Under these circumstances, it is crucial for tree\u27s survival to recover their restricted functionalities quickly after drought release. To elucidate the recovery of carbon (C) transport rates in c. 70-year-old Norway spruce (Picea abies [L.] KARST.) after 5 years of recurrent summer droughts, we conducted a continuous whole-tree $^{13}$C labeling experiment in parallel with watering. We determined the arrival time of current photoassimilates in major C sinks by tracing the $^{13}$C label in stem and soil CO$_{2}$ efflux, and tips of living fine roots. In the first week after watering, aboveground C transport rates (CTR) from crown to trunk base were still 50% lower in previously drought-stressed trees (0.16 ± 0.01 m h$^{-1}$) compared to controls (0.30 ± 0.06 m h$^{-1}$). Conversely, CTR below ground, that is, from the trunk base to soil CO$_{2}$ efflux were already similar between treatments (c. 0.03 m h$^{-1}$). Two weeks after watering, aboveground C transport of previously drought-stressed trees recovered to the level of the controls. Furthermore, regrowth of water-absorbing fine roots upon watering was supported by faster incorporation of $^{13}$C label in previously drought-stressed (within 12 ± 10 h upon arrival at trunk base) compared to control trees (73 ± 10 h). Thus, the whole-tree C transport system from the crown to soil CO$_{2}$ efflux fully recovered within 2 weeks after drought release, and hence showed high resilience to recurrent summer droughts in mature Norway spruce forests. This high resilience of the C transport system is an important prerequisite for the recovery of other tree functionalities and productivity

Dynamics of initial carbon allocation after drought release in mature Norway spruce—Increased belowground allocation of current photoassimilates covers only half of the carbon used for fine‐root growth

After drought events, tree recovery depends on sufficient carbon (C) allocation to the sink organs. The present study aimed to elucidate dynamics of tree-level C sink activity and allocation of recent photoassimilates (C$_{new}$) and stored C in c. 70-year-old Norway spruce (Picea abies) trees during a 4-week period after drought release. We conducted a continuous, whole-tree $^{13}$C labeling in parallel with controlled watering after 5 years of experimental summer drought. The fate of C$_{new}$ to growth and CO$_{2}$ efflux was tracked along branches, stems, coarse- and fine roots, ectomycorrhizae and root exudates to soil CO$_{2}$ efflux after drought release. Compared with control trees, drought recovering trees showed an overall 6% lower C sink activity and 19% less allocation of C$_{new}$ to aboveground sinks, indicating a low priority for aboveground sinks during recovery. In contrast, fine-root growth in recovering trees was seven times greater than that of controls. However, only half of the C used for new fine-root growth was comprised of C$_{new}$ while the other half was supplied by stored C. For drought recovery of mature spruce trees, in addition to C$_{new}$, stored C appears to be critical for the regeneration of the fine-root system and the associated water uptake capacity

Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)

Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TLT was isolated from a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project

Der Einfluss von Trockenheit, Vakuum und Gammastrahlung auf das Überleben thermophiler Mikroorganismen

Die Trockenresistenz verschiedener hitzeliebender Mikroorganismen zeigte unterschiedliche Ausprägungen und unterschritt unter den getesteten Bedingungen nach maximal drei Monaten ein nachweisbares Niveau. Je nach Organismus ergaben sich positive oder negative Abweichungen der Überlebensraten verglichen mit Beblo et al. (2009), worin sich die Komplexität des Phänomens Trockentoleranz zeigt. Weiterhin konnte ein positiver Einfluss von genau definierter Trockenlagerung bei geringer Luftfeuchte auf die Überlebensraten der Testorganismen ermittelt werden, gegenüber einer Lagerung bei mäßiger Luftfeuchte unter weniger stringent kontrollierten Bedingungen. Die Anwesenheit von O₂ während Trocknungsvorgang und Lagerung hatte verglichen mit anoxischen Bedingungen artspezifisch einen absolut tödlichen bis nicht nachweisbaren Effekt. Wurde der Trockenheitsstress nach Beginn der Lagerung durch osmotischen Stress ersetzt, führte dies zu einem beschleunigten Abfall der Überlebensrate. Überdies wirkte O₂ unter diesen Bedingungen schädlicher (bei H. marinus). Eine Erhöhung der Lagertemperatur im Anschluss an den Trocknungsvorgang hatte einen zunehmend negativen Effekt auf die Überlebensrate, eine Erniedrigung der Lagertemperatur einen positiven Effekt (bei H. marinus). Ebenso hatte die Wachstumsphase der Zellen eine Auswirkung auf die Überlebensrate (bei A. fulgidus). Im Gegensatz dazu konnte nach einer bis zu vierwöchigen Exposition gegenüber Ultrahochvakuum kein negativerer Einfluss auf die Testorganismen festgestellt werden, als für Trockenheit bei Normaldruck. Von neun im Vorfeld mit ionisierender Strahlung behandelten Anreicherungen aus marinen Hydrothermalsystemen erwiesen sich sechs als reproduzierbar strahlungstolerant (in Reinkultur). Weiterhin gelang es in einem Vorversuch zwei mikrobielle Kulturen aus einer mit ionisierender Strahlung behandelten Umweltprobe aus dem Umfeld eines schwarzen Rauchers zu gewinnen. Eine dieser Kulturen erwies sich als reproduzierbar strahlungstolerant. Vergleiche zur Phylogenie anhand der Sequenz des 16Sr-RNA Gens ergaben, dass es sich bei den erstgenannten sechs Reinkulturen um Stämme von M. jannaschii, Thermococcus barophilus und Thermococcus gammatolerans handelte. Bei den letzten beiden handelte es sich in Übereinstimmung mit morphologischen Beobachtungen um eine der Gattung Staphylothermus nahestehende, aber vermutlich taxonomisch davon zu trennende Gruppe innerhalb der Desulfurococcaceae und in jedem Fall um Stämme einer neuen Art. Die Ausprägung der Resistenz nach Exposition gegenüber Gammastrahlung (Co-60) war für alle Isolate mit oben erwähnter Ausnahme hoch. Die Nachweisgrenze detektierbaren Überlebens (etwa 99,99999 % Inaktivierung) wurde im Bereich zwischen 10 kGy und mehr als 15 kGy erreicht. Abschließend konnte ein erster Vorversuch eine Korrelation zwischen auf die Zellen applizierter Strahlungsdosis und Amplifikationseffizienz von deren DNA herstellen. Dazu wurde das 16SrRNAGen über qPCR vervielfältigt. Das zu Staphylothermus verwandte Isolat MEX_P besaß den mikroskopischen Befunden nach einige morphologische Besonderheiten. Im Lichtmikroskop wiesen die Zellen gelegentlich im Inneren sowie an ihrer Oberfläche Granula auf und neigten unter suboptimalen Wachstumsbedingungen zur Bildung von Riesenzellen. In elektronenmikroskopischen Präparaten fanden sich neben archaeentypischen Flagellen auch Fibern, deren Aussehen zu keinem bekannten archaeellen Zellanhang verwandt ist, und überdies von Membran und S-layer umschlossene Vesikel. Beide können präparationsbedingte Artefakte darstellen, bei letzteren ist aber eine viral oder zellulär gesteuerte Produktion glaubhaft. Daneben besitzt das Isolat einen in Anbetracht seiner phylogenetischen Stellung ungewöhnlich geordneten S-layer

Characteristic chemical relaxation of induced-fit and conformational-selection binding.

<p>(a) In induced-fit binding, the change between the conformations P₁ and P₂ of the protein occurs after binding of the ligand L. The intermediate state P₁L relaxes into the bound ground state P₂L with rate <i>k</i>_<i>r</i>, and is excited from the ground state with rate <i>k</i>_<i>e</i>. (b) In conformational-selection binding, the conformational change of the protein occurs prior to ligand binding. The intermediate state P₂ is excited from the unbound ground state P₁ with rate <i>k</i>_<i>e</i>, and relaxes back into the ground state with rate <i>k</i>_<i>r</i>. (c) The dominant, smallest relaxation rate <i>k</i>_obs of induced-fit binding is minimal at the total ligand concentration where [P]₀ is the total protein concentration and <i>K</i>_<i>d</i> the overall dissociation constant. As a function of [L]₀, the dominant rate <i>k</i>_obs is symmetric with respect to this minimum. (d) The dominant, smallest relaxation rate <i>k</i>_obs of conformational-selection binding has a characteristic minimum as a function of [L]₀ for <i>k</i>_<i>e</i> > <i>k</i>₋, but is not symmetric with respect to this minimum. (e) The dominant rate <i>k</i>_obs of conformational-selection binding decreases monotonically with [L]₀ for <i>k</i>_<i>e</i> < <i>k</i>₋.</p

Analysis of experimentally determined relaxation rates <i>k</i>_obs for the binding of recoverin to a rhodopsin kinase peptide ligand.

<p>The data points represent results of Chakrabarti et al. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005067#pcbi.1005067.ref028" target="_blank">28</a>] obtained from chemical relaxation experiments at the temperatures 30°C and 10°C for a recoverin concentration of 10 μM. The blue lines result from fits of <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005067#pcbi.1005067.e014" target="_blank">Eq (6)</a> for conformational-selection binding with the values <i>k</i>_<i>r</i> = 1000 s⁻¹ (full) and <i>k</i>_<i>r</i> = 100 s⁻¹ (dashed) of the conformational relaxation rate. At 30°C, the parameter values obtained from fitting are <i>k</i>_<i>e</i> = 31.5 ± 0.8 s⁻¹ and <i>k</i>₋ = 5.1 ± 0.4 s⁻¹ for <i>k</i>_<i>r</i> = 1000 s⁻¹, and <i>k</i>_<i>e</i> = 31.1 ± 0.8 s⁻¹ and <i>k</i>₋ = 5.0 ± 0.4 s⁻¹ for <i>k</i>_<i>r</i> = 100 s⁻¹. At 10°C, the fit parameter values are <i>k</i>_<i>e</i> = 19.3 ± 1.4 s⁻¹ and <i>k</i>₋ = 3.9 ± 0.7 s⁻¹ for <i>k</i>_<i>r</i> = 1000 s⁻¹, and <i>k</i>_<i>e</i> = 19.0 ± 1.3 s⁻¹ and <i>k</i>₋ = 3.8 ± 0.7 s⁻¹ for <i>k</i>_<i>r</i> = 100s⁻¹. The yellow lines represent fits of <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005067#pcbi.1005067.e004" target="_blank">Eq (1)</a> for induced-fit binding with constraints on the conformational excitation and relaxation rates <i>k</i>_<i>e</i> and <i>k</i>_<i>r</i>. At 30°C, the obtained fit values for the conformational exchange rates are <i>k</i>_<i>e</i> = <i>k</i>_<i>r</i> = 15 ± 10 s⁻¹ for the constraint <i>k</i>_<i>r</i> > <i>k</i>_<i>e</i>, <i>k</i>_<i>e</i> = 3.1 ± 1.9 s⁻¹ and <i>k</i>_<i>r</i> = 31 ± 4s⁻¹ for the constraint <i>k</i>_<i>r</i> > 10<i>k</i>_<i>e</i>, and <i>k</i>_<i>e</i> = 1.1 ± 0.8 s⁻¹ and <i>k</i>_<i>r</i> = 44 ± 8 s⁻¹ for <i>k</i>_<i>r</i> > 40<i>k</i>_<i>e</i>. At 10°C, the fit values are <i>k</i>_<i>e</i> = 4.5 ± 4.0 s⁻¹ and <i>k</i>_<i>r</i> = 14 ± 10 s⁻¹ for the constraint <i>k</i>_<i>r</i> > <i>k</i>_<i>e</i>, <i>k</i>_<i>e</i> = 1.9 ± 1.5 s⁻¹ and <i>k</i>_<i>r</i> = 19 ± 5 s⁻¹ for <i>k</i>_<i>r</i> > 10<i>k</i>_<i>e</i>, and <i>k</i>_<i>e</i> = 0.7 ± 0.5 s⁻¹ and <i>k</i>_<i>r</i> = 28 ± 11 s⁻¹ for <i>k</i>_<i>r</i> > 40<i>k</i>_<i>e</i>. In all fits of <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005067#pcbi.1005067.e004" target="_blank">Eq (1)</a> for induced-fit binding, we obtain <i>k</i>₋ ≫ <i>k</i>_<i>r</i>, i.e. the fit values of the unbinding rate <i>k</i>₋ are much larger than the conformational relaxation rate <i>k</i>_<i>r</i> and cannot be specified.</p