TY - JOUR
AB - Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.
AU - Stankowski, Sean
AU - Zagrodzka, Zuzanna B.
AU - Garlovsky, Martin D.
AU - Pal, Arka
AU - Shipilina, Daria
AU - Garcia Castillo, Diego Fernando
AU - Lifchitz, Hila
AU - Le Moan, Alan
AU - Leder, Erica
AU - Reeve, James
AU - Johannesson, Kerstin
AU - Westram, Anja M
AU - Butlin, Roger K.
ID - 14796
IS - 6678
JF - Science
TI - The genetic basis of a recent transition to live-bearing in marine snails
VL - 383
ER -
TY - THES
AB - This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.
Chapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?
Chapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.
Chapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.
Chapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.
AU - Hledik, Michal
ID - 15020
KW - Theoretical biology
KW - Optimality
KW - Evolution
KW - Information
SN - 2663 - 337X
TI - Genetic information and biological optimization
ER -
TY - GEN
AB - Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability.
AU - Benková, Eva
ID - 14842
IS - 1
T2 - Current Biology
TI - Eva Benkova
VL - 34
ER -
TY - JOUR
AB - GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca
2+
-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.
AU - Koppensteiner, Peter
AU - Bhandari, Pradeep
AU - Önal, Hüseyin C
AU - Borges Merjane, Carolina
AU - Le Monnier, Elodie
AU - Roy, Utsa
AU - Nakamura, Yukihiro
AU - Sadakata, Tetsushi
AU - Sanbo, Makoto
AU - Hirabayashi, Masumi
AU - Rhee, JeongSeop
AU - Brose, Nils
AU - Jonas, Peter M
AU - Shigemoto, Ryuichi
ID - 15084
IS - 8
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles
VL - 121
ER -
TY - JOUR
AB - Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation.
AU - Hübner, Valentin
AU - Staab, Manuel
AU - Hilbe, Christian
AU - Chatterjee, Krishnendu
AU - Kleshnina, Maria
ID - 15083
IS - 10
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Efficiency and resilience of cooperation in asymmetric social dilemmas
VL - 121
ER -
TY - GEN
AB - in the research article "Efficiency and resilience of cooperation in asymmetric social dilemmas" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).
We used different implementations for the case of two and three players, both described below.
AU - Hübner, Valentin
AU - Kleshnina, Maria
ID - 15108
TI - Computer code for "Efficiency and resilience of cooperation in asymmetric social dilemmas"
ER -
TY - JOUR
AB - Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.
AU - Schmidt, Hauke
AU - Rast, Sebastian
AU - Bao, Jiawei
AU - Cassim, Amrit
AU - Fang, Shih Wei
AU - Jimenez-De La Cuesta, Diego
AU - Keil, Paul
AU - Kluft, Lukas
AU - Kroll, Clarissa
AU - Lang, Theresa
AU - Niemeier, Ulrike
AU - Schneidereit, Andrea
AU - Williams, Andrew I.L.
AU - Stevens, Bjorn
ID - 15097
IS - 4
JF - Geoscientific Model Development
SN - 1991-959X
TI - Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model
VL - 17
ER -
TY - JOUR
AB - In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.
AU - Naskręcki, Bartosz
AU - Verzobio, Matteo
ID - 12311
JF - Proceedings of the Royal Society of Edinburgh Section A: Mathematics
KW - Elliptic curves
KW - Néron models
KW - division polynomials
KW - height functions
KW - discrete valuation rings
SN - 0308-2105
TI - Common valuations of division polynomials
ER -
TY - JOUR
AB - Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
AU - Johannesson, Kerstin
AU - Faria, Rui
AU - Le Moan, Alan
AU - Rafajlović, Marina
AU - Westram, Anja M
AU - Butlin, Roger K.
AU - Stankowski, Sean
ID - 15099
JF - Trends in Genetics
SN - 0168-9525
TI - Diverse pathways to speciation revealed by marine snails
ER -
TY - JOUR
AB - The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force.
AU - Agresti, Antonio
AU - Luongo, Eliseo
ID - 15098
JF - Mathematische Annalen
SN - 0025-5831
TI - Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions
ER -
TY - JOUR
AB - The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.
AU - Chen, JingJing
AU - Kaufmann, Walter
AU - Chen, Chong
AU - Arai, Itaru
AU - Kim, Olena
AU - Shigemoto, Ryuichi
AU - Jonas, Peter M
ID - 14843
JF - Neuron
SN - 0896-6273
TI - Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse
ER -
TY - THES
AU - Chen, JingJing
ID - 15101
SN - 2663 - 337X
TI - Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse
ER -
TY - JOUR
AB - Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA.
AU - Sack, Stefan
AU - Egger, Daniel J.
ID - 15122
IS - 1
JF - Physical Review Research
SN - 2643-1564
TI - Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation
VL - 6
ER -
TY - JOUR
AB - Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.
AU - Nußbaum, Phillip
AU - Kureisaite-Ciziene, Danguole
AU - Bellini, Dom
AU - Van Der Does, Chris
AU - Kojic, Marko
AU - Taib, Najwa
AU - Yeates, Anna
AU - Tourte, Maxime
AU - Gribaldo, Simonetta
AU - Loose, Martin
AU - Löwe, Jan
AU - Albers, Sonja Verena
ID - 15118
IS - 3
JF - Nature Microbiology
TI - Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division
VL - 9
ER -
TY - JOUR
AB - In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness.
AU - Agresti, Antonio
AU - Veraar, Mark
ID - 15119
IS - 1
JF - Annales de l'institut Henri Poincare Probability and Statistics
SN - 0246-0203
TI - Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions
VL - 60
ER -
TY - JOUR
AB - Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.
AU - Habig, Michael
AU - Grasse, Anna V
AU - Müller, Judith
AU - Stukenbrock, Eva H.
AU - Leitner, Hanna
AU - Cremer, Sylvia
ID - 14478
IS - 11
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Frequent horizontal chromosome transfer between asexual fungal insect pathogens
VL - 121
ER -
TY - JOUR
AB - Given a fixed finite metric space (V,μ), the {\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.
AU - Dvorak, Martin
AU - Kolmogorov, Vladimir
ID - 10045
JF - Mathematical Programming
KW - minimum 0-extension problem
KW - metric labeling problem
KW - discrete metric spaces
KW - metric extensions
KW - computational complexity
KW - valued constraint satisfaction problems
KW - discrete convex analysis
KW - L-convex functions
SN - 0025-5610
TI - Generalized minimum 0-extension problem and discrete convexity
ER -
TY - JOUR
AB - We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges.
AU - Zheng, Da Wei
AU - Henzinger, Monika H
ID - 15121
JF - Mathematical Programming
SN - 0025-5610
TI - Multiplicative auction algorithm for approximate maximum weight bipartite matching
ER -
TY - JOUR
AB - As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.
AU - Yao, Zihao
AU - Liu, Xu
AU - Bunting, Rhys
AU - Wang, Jianguo
ID - 15114
JF - Chemical Engineering Science
SN - 0009-2509
TI - Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling
VL - 291
ER -
TY - JOUR
AB - Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.
AU - Giubertoni, Giulia
AU - Feng, Liru
AU - Klein, Kevin
AU - Giannetti, Guido
AU - Rutten, Luco
AU - Choi, Yeji
AU - Van Der Net, Anouk
AU - Castro-Linares, Gerard
AU - Caporaletti, Federico
AU - Micha, Dimitra
AU - Hunger, Johannes
AU - Deblais, Antoine
AU - Bonn, Daniel
AU - Sommerdijk, Nico
AU - Šarić, Anđela
AU - Ilie, Ioana M.
AU - Koenderink, Gijsje H.
AU - Woutersen, Sander
ID - 15116
IS - 11
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration
VL - 121
ER -