TY - JOUR
AB - Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.
AU - Gauto, Diego F.
AU - Estrozi, Leandro F.
AU - Schwieters, Charles D.
AU - Effantin, Gregory
AU - Macek, Pavel
AU - Sounier, Remy
AU - Sivertsen, Astrid C.
AU - Schmidt, Elena
AU - Kerfah, Rime
AU - Mas, Guillaume
AU - Colletier, Jacques-Philippe
AU - Güntert, Peter
AU - Favier, Adrien
AU - Schoehn, Guy
AU - Schanda, Paul
AU - Boisbouvier, Jerome
ID - 8405
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex
VL - 10
ER -
TY - JOUR
AB - Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation.
AU - Felix, Jan
AU - Weinhäupl, Katharina
AU - Chipot, Christophe
AU - Dehez, François
AU - Hessel, Audrey
AU - Gauto, Diego F.
AU - Morlot, Cecile
AU - Abian, Olga
AU - Gutsche, Irina
AU - Velazquez-Campoy, Adrian
AU - Schanda, Paul
AU - Fraga, Hugo
ID - 8406
IS - 9
JF - Science Advances
SN - 2375-2548
TI - Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors
VL - 5
ER -
TY - JOUR
AU - Schanda, Paul
ID - 8407
JF - Journal of Magnetic Resonance
KW - Nuclear and High Energy Physics
KW - Biophysics
KW - Biochemistry
KW - Condensed Matter Physics
SN - 1090-7807
TI - Relaxing with liquids and solids – A perspective on biomolecular dynamics
VL - 306
ER -
TY - JOUR
AB - Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.
AU - Gauto, Diego F.
AU - Macek, Pavel
AU - Barducci, Alessandro
AU - Fraga, Hugo
AU - Hessel, Audrey
AU - Terauchi, Tsutomu
AU - Gajan, David
AU - Miyanoiri, Yohei
AU - Boisbouvier, Jerome
AU - Lichtenecker, Roman
AU - Kainosho, Masatsune
AU - Schanda, Paul
ID - 8408
IS - 28
JF - Journal of the American Chemical Society
KW - Colloid and Surface Chemistry
KW - Biochemistry
KW - General Chemistry
KW - Catalysis
SN - 0002-7863
TI - Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR
VL - 141
ER -
TY - JOUR
AB - The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling.
AU - Bougault, Catherine
AU - Ayala, Isabel
AU - Vollmer, Waldemar
AU - Simorre, Jean-Pierre
AU - Schanda, Paul
ID - 8409
IS - 1
JF - Journal of Structural Biology
KW - Structural Biology
SN - 1047-8477
TI - Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency
VL - 206
ER -
TY - JOUR
AU - Schanda, Paul
AU - Chekmenev, Eduard Y.
ID - 8410
IS - 2
JF - ChemPhysChem
SN - 1439-4235
TI - NMR for Biological Systems
VL - 20
ER -
TY - JOUR
AB - Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.
AU - Marion, Dominique
AU - Gauto, Diego F.
AU - Ayala, Isabel
AU - Giandoreggio-Barranco, Karine
AU - Schanda, Paul
ID - 8411
IS - 2
JF - ChemPhysChem
KW - Physical and Theoretical Chemistry
KW - Atomic and Molecular Physics
KW - and Optics
SN - 1439-4235
TI - Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR
VL - 20
ER -
TY - JOUR
AB - Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.
AU - Shannon, Matthew D.
AU - Theint, Theint
AU - Mukhopadhyay, Dwaipayan
AU - Surewicz, Krystyna
AU - Surewicz, Witold K.
AU - Marion, Dominique
AU - Schanda, Paul
AU - Jaroniec, Christopher P.
ID - 8412
IS - 2
JF - ChemPhysChem
KW - Physical and Theoretical Chemistry
KW - Atomic and Molecular Physics
KW - and Optics
SN - 1439-4235
TI - Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR
VL - 20
ER -
TY - JOUR
AB - NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains.
AU - Rovó, Petra
AU - Smith, Colin A.
AU - Gauto, Diego
AU - de Groot, Bert L.
AU - Schanda, Paul
AU - Linser, Rasmus
ID - 8413
IS - 2
JF - Journal of the American Chemical Society
KW - Colloid and Surface Chemistry
KW - Biochemistry
KW - General Chemistry
KW - Catalysis
SN - 0002-7863
TI - Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques
VL - 141
ER -
TY - JOUR
AB - We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit.
AU - Bálint, Péter
AU - De Simoi, Jacopo
AU - Kaloshin, Vadim
AU - Leguil, Martin
ID - 8415
IS - 3
JF - Communications in Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0010-3616
TI - Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards
VL - 374
ER -
TY - JOUR
AB - In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.
AU - Huang, Guan
AU - Kaloshin, Vadim
ID - 8416
IS - 2
JF - Moscow Mathematical Journal
SN - 1609-4514
TI - On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables
VL - 19
ER -
TY - JOUR
AB - For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0.
AU - Guardia, Marcel
AU - Kaloshin, Vadim
AU - Zhang, Jianlu
ID - 8418
IS - 2
JF - Archive for Rational Mechanics and Analysis
KW - Mechanical Engineering
KW - Mathematics (miscellaneous)
KW - Analysis
SN - 0003-9527
TI - Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem
VL - 233
ER -
TY - CONF
AB - This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.
AU - Althoff, Matthias
AU - Bak, Stanley
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Kochdumper, Niklas
AU - Ray, Rajarshi
AU - Schilling, Christian
AU - Schupp, Stefan
ID - 8570
T2 - EPiC Series in Computing
TI - ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics
VL - 61
ER -
TY - JOUR
AB - We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed.
AU - Chierchia, Luigi
AU - Koudjinan, Edmond
ID - 8693
JF - Regular and Chaotic Dynamics
TI - V. I. Arnold’s “pointwise” KAM theorem
VL - 24
ER -
TY - JOUR
AB - Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ .
AU - Browning, Timothy D
AU - Sofos, Efthymios
ID - 170
IS - 3-4
JF - Mathematische Annalen
TI - Counting rational points on quartic del Pezzo surfaces with a rational conic
VL - 373
ER -
TY - JOUR
AB - An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.
AU - Browning, Timothy D
AU - Loughran, Daniel
ID - 175
IS - 8
JF - Transactions of the American Mathematical Society
SN - 00029947
TI - Sieving rational points on varieties
VL - 371
ER -
TY - JOUR
AB - The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain.
AU - Lang, Moritz
AU - Shkolnikov, Mikhail
ID - 196
IS - 8
JF - Proceedings of the National Academy of Sciences
TI - Harmonic dynamics of the Abelian sandpile
VL - 116
ER -
TY - JOUR
AB - Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.
AU - Vicoso, Beatriz
ID - 7146
IS - 12
JF - Nature Ecology & Evolution
SN - 2397-334X
TI - Molecular and evolutionary dynamics of animal sex-chromosome turnover
VL - 3
ER -
TY - CONF
AB - The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.
In this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.
The behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions.
AU - Guet, Calin C
AU - Henzinger, Thomas A
AU - Igler, Claudia
AU - Petrov, Tatjana
AU - Sezgin, Ali
ID - 7147
SN - 0302-9743
T2 - 17th International Conference on Computational Methods in Systems Biology
TI - Transient memory in gene regulation
VL - 11773
ER -
TY - JOUR
AB - In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include:
1. triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm of Dolev et al. [DISC 2012],
2. a (1+o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation algorithm given by Nanongkai [STOC 2014], and
3. computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model.
In addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles.
AU - Censor-Hillel, Keren
AU - Kaski, Petteri
AU - Korhonen, Janne
AU - Lenzen, Christoph
AU - Paz, Ami
AU - Suomela, Jukka
ID - 7150
IS - 6
JF - Distributed Computing
SN - 0178-2770
TI - Algebraic methods in the congested clique
VL - 32
ER -