Frédéric Poitevin
Staff Scientist, SLAC National Accelerator Laboratory
https://orcid.org/0000-0002-3181-8652All Publications
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Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations.
Frontiers in molecular biosciences
2024; 11: 1393564
Abstract
Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.
View details for DOI 10.3389/fmolb.2024.1393564
View details for PubMedID 39044842
View details for PubMedCentralID PMC11263974
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Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.
Science advances
2024; 10 (13): eadk7201
Abstract
Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.
View details for DOI 10.1126/sciadv.adk7201
View details for PubMedID 38536910
View details for PubMedCentralID PMC10971408
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Structural biology in the age of X-ray free-electron lasers and exascale computing.
Current opinion in structural biology
2024; 86: 102808
Abstract
Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, we can now rapidly probe ultrafast conformational changes and charge movement in biomolecules. Over the last year, another innovation has been the deployment of Frontier, the world's first exascale supercomputer. Synergizing extremely high repetition rate X-ray light sources and exascale computing has the potential to accelerate discovery in biomolecular sciences. Here we outline our perspective on each of these remarkable innovations individually, and the opportunities and challenges in yoking them within an integrated research infrastructure.
View details for DOI 10.1016/j.sbi.2024.102808
View details for PubMedID 38547555
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AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps.
IEEE/ACM transactions on computational biology and bioinformatics
2023; 20 (6): 3842-3850
Abstract
Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. We quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.
View details for DOI 10.1109/TCBB.2023.3327633
View details for PubMedID 37889827
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RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers
SCIENCE ADVANCES
2023; 9 (39): eadj3509
Abstract
RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.
View details for DOI 10.1126/sciadv.adj3509
View details for Web of Science ID 001076013000012
View details for PubMedID 37756398
View details for PubMedCentralID PMC10530093
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Structural insights into functional properties of the oxidized form of cytochrome c oxidase.
Nature communications
2023; 14 (1): 5752
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.
View details for DOI 10.1038/s41467-023-41533-x
View details for PubMedID 37717031
View details for PubMedCentralID 6203177
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Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.
bioRxiv : the preprint server for biology
2023
Abstract
Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and time-resolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.
View details for DOI 10.1101/2023.08.15.553460
View details for PubMedID 37645800
View details for PubMedCentralID PMC10462001
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Modeling diffuse scattering with simple, physically interpretable models.
Methods in enzymology
2023; 688: 169-194
Abstract
Diffuse scattering has long been proposed to probe protein dynamics relevant for biological function, and more recently, as a tool to aid structure determination. Despite recent advances in measuring and modeling this signal, the field has not been able to routinely use experimental diffuse scattering for either application. A persistent challenge has been to devise models that are sophisticated enough to robustly reproduce experimental diffuse features but remain readily interpretable from the standpoint of structural biology. This chapter presents eryx, a suite of computational tools to evaluate the primary models of disorder that have been used to analyze protein diffuse scattering. By facilitating comparative modeling, eryx aims to provide insights into the physical origins of this signal and help identify the sources of disorder that are critical for reproducing experimental features. This framework also lays the groundwork for the development of more advanced models that integrate different types of disorder without loss of interpretability.
View details for DOI 10.1016/bs.mie.2023.06.022
View details for PubMedID 37748826
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Amortized Inference for Heterogeneous Reconstruction in Cryo-EM.
Advances in neural information processing systems
2022; 35: 13038-13049
Abstract
Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights into the dynamics of proteins and other building blocks of life. The algorithmic challenge of jointly estimating the poses, 3D structure, and conformational heterogeneity of a biomolecule from millions of noisy and randomly oriented 2D projections in a computationally efficient manner, however, remains unsolved. Our method, cryoFIRE, performs ab initio heterogeneous reconstruction with unknown poses in an amortized framework, thereby avoiding the computationally expensive step of pose search while enabling the analysis of conformational heterogeneity. Poses and conformation are jointly estimated by an encoder while a physics-based decoder aggregates the images into an implicit neural representation of the conformational space. We show that our method can provide one order of magnitude speedup on datasets containing millions of images without any loss of accuracy. We validate that the joint estimation of poses and conformations can be amortized over the size of the dataset. For the first time, we prove that an amortized method can extract interpretable dynamic information from experimental datasets.
View details for PubMedID 37529401
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Deep Generative Modeling for Volume Reconstruction in Cryo-Electron Microscopy.
Journal of structural biology
2022: 107920
Abstract
Advances in cryo-electron microscopy (cryo-EM) for high-resolution imaging of biomolecules in solution have provided new challenges and opportunities for algorithm development for 3D reconstruction. Next-generation volume reconstruction algorithms that combine generative modelling with end-to-end unsupervised deep learning techniques have shown promise, but many technical and theoretical hurdles remain, especially when applied to experimental cryo-EM images. In light of the proliferation of such methods, we propose here a critical review of recent advances in the field of deep generative modelling for cryo-EM reconstruction. The present review aims to (i) provide a unified statistical framework using terminology familiar to machine learning researchers with no specific background in cryo-EM, (ii) review the current methods in this framework, and (iii) outline outstanding bottlenecks and avenues for improvements in the field.
View details for DOI 10.1016/j.jsb.2022.107920
View details for PubMedID 36356882
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CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images.
Computer vision - ECCV ... : ... European Conference on Computer Vision : proceedings. European Conference on Computer Vision
2022; 13681: 540-557
Abstract
Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses and the 3D electron scattering potential of a biomolecule from millions of extremely noisy 2D images. Existing reconstruction algorithms, however, cannot easily keep pace with the rapidly growing size of cryo-EM datasets due to their high computational and memory cost. We introduce cryoAI, an ab initio reconstruction algorithm for homogeneous conformations that uses direct gradient-based optimization of particle poses and the electron scattering potential from single-particle cryo-EM data. CryoAI combines a learned encoder that predicts the poses of each particle image with a physics-based decoder to aggregate each particle image into an implicit representation of the scattering potential volume. This volume is stored in the Fourier domain for computational efficiency and leverages a modern coordinate network architecture for memory efficiency. Combined with a symmetrized loss function, this framework achieves results of a quality on par with state-of-the-art cryo-EM solvers for both simulated and experimental data, one order of magnitude faster for large datasets and with significantly lower memory requirements than existing methods.
View details for DOI 10.1007/978-3-031-19803-8_32
View details for PubMedID 36745134
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Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography.
STAR protocols
2022; 3 (1): 101158
Abstract
The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography. For complete details on the use and execution of this protocol, please refer to Durdagi etal. (2021).
View details for DOI 10.1016/j.xpro.2022.101158
View details for PubMedID 35194584
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Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature.
Communications biology
1800; 5 (1): 73
Abstract
Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7A resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1A resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.
View details for DOI 10.1038/s42003-021-02903-7
View details for PubMedID 35058563
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Chemical crystallography by serial femtosecond X-ray diffraction.
Nature
1800; 601 (7893): 360-365
Abstract
Inorganic-organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties1. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction2,3 and electron microdiffraction4-11. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powderdiffractograms. After indexing the sparse serial patterns by a graph theory approach14, the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data15-17. We describe the ab initio structure solutions of mithrene (AgSePh)18-20, thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver-silver bonding network that is linked to its divergent optoelectronic properties20. We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.
View details for DOI 10.1038/s41586-021-04218-3
View details for PubMedID 35046599
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Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
CRYSTALS
2021; 11 (12)
View details for DOI 10.3390/cryst11121579
View details for Web of Science ID 000739687500001
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Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.
Structure (London, England : 1993)
2021
Abstract
The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.
View details for DOI 10.1016/j.str.2021.07.007
View details for PubMedID 34403647
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Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.
Structural dynamics (Melville, N.Y.)
2021; 8 (4): 044701
Abstract
Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
View details for DOI 10.1063/4.0000087
View details for PubMedID 34258328
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Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6.
Molecular cell
2020
Abstract
Heterotrimeric G proteins communicate signals from activated G protein-coupled receptors to downstream effector proteins. In the phototransduction pathway responsible for vertebrate vision, the G protein-effector complex is composed of the GTP-bound transducin alpha subunit (GalphaT·GTP) and the cyclic GMP (cGMP) phosphodiesterase 6 (PDE6), which stimulates cGMP hydrolysis, leading to hyperpolarization of the photoreceptor cell. Here we report a cryo-electron microscopy (cryoEM) structure of PDE6 complexed to GTP-bound GalphaT. The structure reveals two GalphaT·GTP subunits engaging the PDE6 hetero-tetramer at both the PDE6 catalytic core and the PDEgamma subunits, driving extensive rearrangements to relieve all inhibitory constraints on enzyme catalysis. Analysis of the conformational ensemble in the cryoEM data highlights the dynamic nature of the contacts between the two GalphaT·GTP subunits and PDE6 that supports an alternating-site catalytic mechanism.
View details for DOI 10.1016/j.molcel.2020.09.013
View details for PubMedID 33007200
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Structure of the 30S ribosomal decoding complex at ambient temperature
RNA
2018; 24 (12): 1667–76
View details for DOI 10.1261/rna.067660.118
View details for Web of Science ID 000450373800006
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Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature
NUCLEIC ACIDS RESEARCH
2018; 46 (18): 9793–9804
View details for DOI 10.1093/nar/gky693
View details for Web of Science ID 000450953200048
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Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins
ISME JOURNAL
2018; 12 (10): 2389–2402
View details for DOI 10.1038/s41396-018-0191-0
View details for Web of Science ID 000445254300005
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Structure of the 30S ribosomal decoding complex at ambient temperature.
RNA (New York, N.Y.)
2018
Abstract
The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 A resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation to structural studies of RNA and RNA-protein complexes at near-physiological temperatures.
View details for PubMedID 30139800
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Atomistic string method solution for ion channel gating and modulation by general anesthetics
AMER CHEMICAL SOC. 2018
View details for Web of Science ID 000447600004477
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Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature.
Nucleic acids research
2018
Abstract
The bacterial 30S ribosomal subunit is a primary antibiotic target. Despite decades of discovery, the mechanisms by which antibiotic binding induces ribosomal dysfunction are not fully understood. Ambient temperature crystallographic techniques allow more biologically relevant investigation of how local antibiotic binding site interactions trigger global subunit rearrangements that perturb protein synthesis. Here, the structural effects of 2-deoxystreptamine (paromomycin and sisomicin), a novel sisomicin derivative, N1-methyl sulfonyl sisomicin (N1MS) and the non-deoxystreptamine (streptomycin) aminoglycosides on the ribosome at ambient and cryogenic temperatures were examined. Comparative studies led to three main observations. First, individual aminoglycoside-ribosome interactions in the decoding center were similar for cryogenic versus ambient temperature structures. Second, analysis of a highly conserved GGAA tetraloop of h45 revealed aminoglycoside-specific conformational changes, which are affected by temperature only for N1MS. We report the h44-h45 interface in varying states, i.e. engaged, disengaged and in equilibrium. Third, we observe aminoglycoside-induced effects on 30S domain closure, including a novel intermediary closure state, which is also sensitive to temperature. Analysis of three ambient and five cryogenic crystallography datasets reveal a correlation between h44-h45 engagement and domain closure. These observations illustrate the role of ambient temperature crystallography in identifying dynamic mechanisms of ribosomal dysfunction induced by local drug-binding site interactions. Together, these data identify tertiary ribosomal structural changes induced by aminoglycoside binding that provides functional insight and targets for drug design.
View details for PubMedID 30113694
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Intermolecular correlations are necessary to explain diffuse scattering from protein crystals
IUCRJ
2018; 5: 211–22
Abstract
Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.
View details for PubMedID 29765611
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Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins.
The ISME journal
2018
Abstract
Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.
View details for PubMedID 29899515
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Reduction of small-angle scattering profiles to finite sets of structural invariants
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
2017; 73: 317–32
Abstract
This paper shows how small-angle scattering (SAS) curves can be decomposed in a simple sum using a set of invariant parameters called Kn which are related to the shape of the object of study. These Kn, together with a radius R, give a complete theoretical description of the SAS curve. Adding an overall constant, these parameters are easily fitted against experimental data giving a concise comprehensive description of the data. The pair distance distribution function is also entirely described by this invariant set and the Dmax parameter can be measured. In addition to the understanding they bring, these invariants can be used to reliably estimate structural moments beyond the radius of gyration, thereby rigorously expanding the actual set of model-free quantities one can extract from experimental SAS data, and possibly paving the way to designing new shape reconstruction strategies.
View details for DOI 10.1107/S205327331700451X
View details for Web of Science ID 000404590700005
View details for PubMedID 28660864
View details for PubMedCentralID PMC5571748
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String method solution of the gating pathways for a pentameric ligand-gated ion channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2017; 114 (21): E4158-E4167
Abstract
Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.
View details for DOI 10.1073/pnas.1617567114
View details for Web of Science ID 000401797800009
View details for PubMedID 28487483
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The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.
Journal of chemical theory and computation
2017
Abstract
Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.
View details for DOI 10.1021/acs.jctc.6b01136
View details for PubMedID 28170254
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Gating Pathways for a Pentameric Ligand-Gated Ion Channel Solved by Atomistic String Method Simulations
CELL PRESS. 2017: 475A
View details for DOI 10.1016/j.bpj.2016.11.2553
View details for Web of Science ID 000402375700349
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Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations
JOURNAL OF PHYSICAL CHEMISTRY B
2016; 120 (26): 6270-6277
Abstract
We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the mean-field solution given by the Poisson-Boltzmann equation, an original approach is proposed to numerically sample fluctuations around it, through the propagation of a Langevin-like stochastic partial differential equation (SPDE). The diffusion tensor of the SPDE can be chosen so as to avoid the numerical complexity linked to long-range Coulomb interactions, effectively rendering the theory completely local. A finite-volume implementation of the SPDE is described, and the approach is illustrated with preliminary results on the study of a system made of two like-charge ions immersed in a bath of counterions.
View details for DOI 10.1021/acs.jpcb.6b02650
View details for Web of Science ID 000379457200055
View details for PubMedID 27075231
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Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.
Frontiers in molecular biosciences
2016; 3: 85-?
Abstract
Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis. We describe the elements of DD-NMA that are relevant to the analysis of large systems, such as virus capsids. In particular, we introduce our implementation of simplified elastic networks and justify their parametrization. Using DD-NMA, we illustrate the importance of packing interactions within the virus capsids on the dynamics of the E proteins of DENV and ZIKV. We identify differences between the computed atomic fluctuations of the E proteins in DENV and ZIKV and relate those differences to changes observed in their high resolution structures. We conclude with a discussion on additional analyses that are needed to fully characterize the dynamics of the two viruses.
View details for DOI 10.3389/fmolb.2016.00085
View details for PubMedID 28083537
View details for PubMedCentralID PMC5187361
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AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models
NUCLEIC ACIDS RESEARCH
2011; 39: W184-W189
Abstract
Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php).
View details for DOI 10.1093/nar/gkr430
View details for Web of Science ID 000292325300031
View details for PubMedID 21665925
View details for PubMedCentralID PMC3125794