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Wang RYR, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 2016; 5. [PMID: 27669148 PMCID: PMC5115868 DOI: 10.7554/elife.17219] [Citation(s) in RCA: 375] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/22/2016] [Indexed: 01/25/2023] Open
Abstract
Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3–4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps. DOI:http://dx.doi.org/10.7554/eLife.17219.001
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Research Support, N.I.H., Extramural |
9 |
375 |
2
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Cabezón E, Ripoll-Rozada J, Peña A, de la Cruz F, Arechaga I. Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 2014; 39:81-95. [PMID: 25154632 DOI: 10.1111/1574-6976.12085] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial conjugation is one of the main mechanisms for horizontal gene transfer. It constitutes a key element in the dissemination of antibiotic resistance and virulence genes to human pathogenic bacteria. DNA transfer is mediated by a membrane-associated macromolecular machinery called Type IV secretion system (T4SS). T4SSs are involved not only in bacterial conjugation but also in the transport of virulence factors by pathogenic bacteria. Thus, the search for specific inhibitors of different T4SS components opens a novel approach to restrict plasmid dissemination. This review highlights recent biochemical and structural findings that shed new light on the molecular mechanisms of DNA and protein transport by T4SS. Based on these data, a model for pilus biogenesis and substrate transfer in conjugative systems is proposed. This model provides a renewed view of the mechanism that might help to envisage new strategies to curb the threating expansion of antibiotic resistance.
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Review |
11 |
127 |
3
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Lasker K, Topf M, Sali A, Wolfson HJ. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol 2009; 388:180-94. [PMID: 19233204 PMCID: PMC2680734 DOI: 10.1016/j.jmb.2009.02.031] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Revised: 12/29/2008] [Accepted: 02/12/2009] [Indexed: 11/24/2022]
Abstract
Models of macromolecular assemblies are essential for a mechanistic description of cellular processes. Such models are increasingly obtained by fitting atomic-resolution structures of components into a density map of the whole assembly. Yet, current density-fitting techniques are frequently insufficient for an unambiguous determination of the positions and orientations of all components. Here, we describe MultiFit, a method used for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25 A. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, and the shape complementarity between pairs of components. The scoring function is optimized by our exact inference optimizer DOMINO (Discrete Optimization of Multiple INteracting Objects) that efficiently finds the global minimum in a discrete sampling space. MultiFit was benchmarked on seven assemblies of known structure, consisting of up to seven proteins each. The input atomic structures of the components were obtained from the Protein Data Bank, as well as by comparative modeling based on a 16-99% sequence identity to a template structure. A near-native configuration was usually found as the top-scoring model. Therefore, MultiFit can provide initial configurations for further refinement of many multicomponent assembly structures described by electron microscopy.
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Research Support, N.I.H., Extramural |
16 |
97 |
4
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Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in integrative structural modeling. Curr Opin Struct Biol 2014; 28:96-104. [PMID: 25173450 PMCID: PMC4252396 DOI: 10.1016/j.sbi.2014.08.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/24/2014] [Accepted: 08/05/2014] [Indexed: 01/08/2023]
Abstract
Integrative structural modeling uses multiple types of input information and proceeds in four stages: (i) gathering information, (ii) designing model representation and converting information into a scoring function, (iii) sampling good-scoring models, and (iv) analyzing models and information. In the first stage, uncertainty originates from data that are sparse, noisy, ambiguous, or derived from heterogeneous samples. In the second stage, uncertainty can originate from a representation that is too coarse for the available information or a scoring function that does not accurately capture the information. In the third stage, the major source of uncertainty is insufficient sampling. In the fourth stage, clustering, cross-validation, and other methods are used to estimate the precision and accuracy of the models and information.
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Research Support, N.I.H., Extramural |
11 |
81 |
5
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Sousa AA, Leapman RD. Development and application of STEM for the biological sciences. Ultramicroscopy 2012; 123:38-49. [PMID: 22749213 PMCID: PMC3500455 DOI: 10.1016/j.ultramic.2012.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 04/06/2012] [Accepted: 04/13/2012] [Indexed: 01/06/2023]
Abstract
The design of the scanning transmission electron microscope (STEM), as conceived originally by Crewe and coworkers, enables the highly efficient and flexible collection of different elastic and inelastic signals resulting from the interaction of a focused probe of incident electrons with a specimen. In the present paper we provide a brief review for how the STEM today can be applied towards a range of different problems in the biological sciences, emphasizing four main areas of application. (1) For three decades, the most widely used STEM technique has been the mass determination of proteins and other macromolecular assemblies. Such measurements can be performed at low electron dose by collecting the high-angle dark-field signal using an annular detector. STEM mass mapping has proven valuable for characterizing large protein assemblies such as filamentous proteins with a well-defined mass per length. (2) The annular dark-field signal can also be used to image ultrasmall, functionalized nanoparticles of heavy atoms for labeling specific amino-acid sequences in protein assemblies. (3) By acquiring electron energy loss spectra (EELS) at each pixel in a hyperspectral image, it is possible to map the distributions of specific bound elements like phosphorus, calcium and iron in isolated macromolecular assemblies or in compartments within sectioned cells. Near single atom sensitivity is feasible provided that the specimen can tolerate a very high incident electron dose. (4) Electron tomography is a new application of STEM that enables three-dimensional reconstruction of micrometer-thick sections of cells. In this technique a probe of small convergence angle gives a large depth of field throughout the thickness of the specimen while maintaining a probe diameter of <2 nm; and the use of an on-axis bright-field detector reduces the effects of beam broadening and thus improves the spatial resolution compared to that attainable by STEM dark-field tomography.
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Research Support, N.I.H., Intramural |
13 |
54 |
6
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Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family. Proc Natl Acad Sci U S A 2014; 111:1837-42. [PMID: 24449904 DOI: 10.1073/pnas.1319848111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinesins are responsible for a wide variety of microtubule-based, ATP-dependent functions. Their motor domain drives these activities, but the molecular adaptations that specify these diverse and essential cellular activities are poorly understood. It has been assumed that the first identified kinesin--the transport motor kinesin-1--is the mechanistic paradigm for the entire superfamily, but accumulating evidence suggests otherwise. To address the deficits in our understanding of the molecular basis of functional divergence within the kinesin superfamily, we studied kinesin-5s, which are essential mitotic motors whose inhibition blocks cell division. Using cryo-electron microscopy and determination of structure at subnanometer resolution, we have visualized conformations of microtubule-bound human kinesin-5 motor domain at successive steps in its ATPase cycle. After ATP hydrolysis, nucleotide-dependent conformational changes in the active site are allosterically propagated into rotations of the motor domain and uncurling of the drug-binding loop L5. In addition, the mechanical neck-linker element that is crucial for motor stepping undergoes discrete, ordered displacements. We also observed large reorientations of the motor N terminus that indicate its importance for kinesin-5 function through control of neck-linker conformation. A kinesin-5 mutant lacking this N terminus is enzymatically active, and ATP-dependent neck-linker movement and motility are defective, although not ablated. All these aspects of kinesin-5 mechanochemistry are distinct from kinesin-1. Our findings directly demonstrate the regulatory role of the kinesin-5 N terminus in collaboration with the motor's structured neck-linker and highlight the multiple adaptations within kinesin motor domains that tune their mechanochemistries according to distinct functional requirements.
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Research Support, Non-U.S. Gov't |
11 |
47 |
7
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Rothnie A, Clarke AR, Kuzmic P, Cameron A, Smith CJ. A sequential mechanism for clathrin cage disassembly by 70-kDa heat-shock cognate protein (Hsc70) and auxilin. Proc Natl Acad Sci U S A 2011; 108:6927-32. [PMID: 21482805 PMCID: PMC3084117 DOI: 10.1073/pnas.1018845108] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An essential stage in endocytic coated vesicle recycling is the dissociation of clathrin from the vesicle coat by the molecular chaperone, 70-kDa heat-shock cognate protein (Hsc70), and the J-domain-containing protein, auxilin, in an ATP-dependent process. We present a detailed mechanistic analysis of clathrin disassembly catalyzed by Hsc70 and auxilin, using loss of perpendicular light scattering to monitor the process. We report that a single auxilin per clathrin triskelion is required for maximal rate of disassembly, that ATP is hydrolyzed at the same rate that disassembly occurs, and that three ATP molecules are hydrolyzed per clathrin triskelion released. Stopped-flow measurements revealed a lag phase in which the scattering intensity increased owing to association of Hsc70 with clathrin cages followed by serial rounds of ATP hydrolysis prior to triskelion removal. Global fit of stopped-flow data to several physically plausible mechanisms showed the best fit to a model in which sequential hydrolysis of three separate ATP molecules is required for the eventual release of a triskelion from the clathrin-auxilin cage.
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research-article |
14 |
46 |
8
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NMR mapping of PCNA interaction with translesion synthesis DNA polymerase Rev1 mediated by Rev1-BRCT domain. J Mol Biol 2013; 425:3091-105. [PMID: 23747975 DOI: 10.1016/j.jmb.2013.05.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 05/13/2013] [Accepted: 05/30/2013] [Indexed: 01/13/2023]
Abstract
Rev1 is a Y-family translesion synthesis (TLS) DNA polymerase involved in bypass replication across sites of DNA damage and postreplicational gap filling. In the process of TLS, high-fidelity replicative DNA polymerases stalled by DNA damage are replaced by error-prone TLS enzymes responsible for the majority of mutagenesis in eukaryotic cells. The polymerase exchange that gains low-fidelity TLS polymerases access to DNA is mediated by their interactions with proliferating cell nuclear antigen (PCNA). Rev1 stands alone from other Y-family TLS enzymes since it lacks the consensus PCNA-interacting protein box (PIP-box) motif, instead utilizing other modular domains for PCNA binding. Here we report solution NMR structure of an 11-kDa BRCA1 C-terminus (BRCT) domain from Saccharomyces cerevisiae Rev1 and demonstrate with the use of transverse relaxation optimized spectroscopy (TROSY) NMR methods that Rev1-BRCT domain directly interacts with an 87-kDa PCNA in solution. The domain adopts α/β fold (β1-α1-β2-β3-α2-β4-α3-α4) typical for BRCT domain superfamily. PCNA-binding interface of the Rev1-BRCT domain comprises conserved residues of the outer surface of the α1-helix and the α1-β1, β2-β3 and β3-α2 loops. On the other hand, Rev1-BRCT binds to the inter-domain region of PCNA that overlaps with the binding site for the PIP-box motif. Furthermore, Rev1-BRCT domain bound to PCNA can be displaced by increasing amounts of the PIP-box peptide from TLS DNA polymerase polη, suggesting that Rev1-BRCT and polη PIP-box interactions with the same PCNA monomer are mutually exclusive. These results provide structural insights into PCNA recognition by TLS DNA polymerases that help better understand TLS regulation in eukaryotes.
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Research Support, Non-U.S. Gov't |
12 |
40 |
9
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Braitbard M, Schneidman-Duhovny D, Kalisman N. Integrative Structure Modeling: Overview and Assessment. Annu Rev Biochem 2019; 88:113-135. [PMID: 30830798 DOI: 10.1146/annurev-biochem-013118-111429] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Integrative structure modeling computationally combines data from multiple sources of information with the aim of obtaining structural insights that are not revealed by any single approach alone. In the first part of this review, we survey the commonly used sources of structural information and the computational aspects of model building. Throughout the past decade, integrative modeling was applied to various biological systems, with a focus on large protein complexes. Recent progress in the field of cryo-electron microscopy (cryo-EM) has resolved many of these complexes to near-atomic resolution. In the second part of this review, we compare a range of published integrative models with their higher-resolution counterparts with the aim of critically assessing their accuracy. This comparison gives a favorable view of integrative modeling and demonstrates its ability to yield accurate and informative results. We discuss possible roles of integrative modeling in the new era of cryo-EM and highlight future challenges and directions.
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Review |
6 |
36 |
10
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Hosseinizadeh A, Schwander P, Dashti A, Fung R, D'Souza RM, Ourmazd A. High-resolution structure of viruses from random diffraction snapshots. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130326. [PMID: 24914154 PMCID: PMC4052863 DOI: 10.1098/rstb.2013.0326] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects.
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Research Support, U.S. Gov't, Non-P.H.S. |
10 |
32 |
11
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Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F. Exploring the spatial and temporal organization of a cell's proteome. J Struct Biol 2011; 173:483-96. [PMID: 21094684 PMCID: PMC3784337 DOI: 10.1016/j.jsb.2010.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 11/05/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
To increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. These levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and spatial distribution in the cell. Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells. This review addresses three fields that have significantly contributed to our understanding of the proteome's spatial and temporal organization: first, methods for the structure determination of individual macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of these complexes within the cellular context using cryo electron tomography techniques combined with computational image processing; and third, methods for the spatial modeling of the dynamic organization of the proteome, specifically those methods for simulating reaction and diffusion of proteins and complexes in crowded intracellular fluids. The long-term goal is to integrate the varied data about a proteome's organization into a spatially explicit, predictive model of cellular processes.
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Research Support, N.I.H., Extramural |
14 |
25 |
12
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Dror O, Lasker K, Nussinov R, Wolfson H. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007; 63:42-9. [PMID: 17164525 PMCID: PMC2483490 DOI: 10.1107/s0907444906041059] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 10/08/2006] [Indexed: 11/22/2022]
Abstract
Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.
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Research Support, N.I.H., Extramural |
18 |
17 |
13
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Haldrup K. Singular value decomposition as a tool for background corrections in time-resolved XFEL scattering data. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130336. [PMID: 24914162 DOI: 10.1098/rstb.2013.0336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of new X-ray light sources, XFELs, with unprecedented time and brilliance characteristics has led to the availability of very large datasets with high time resolution and superior signal strength. The chaotic nature of the emission processes in such sources as well as entirely novel detector demands has also led to significant challenges in terms of data analysis. This paper describes a heuristic approach to datasets where spurious background contributions of a magnitude similar to (or larger) than the signal of interest prevents conventional analysis approaches. The method relies on singular-value decomposition of no-signal subsets of acquired datasets in combination with model inputs and appears generally applicable to time-resolved X-ray diffuse scattering experiments.
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14 |
14
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Simon AJ, Walls-Smith LT, Freddi MJ, Fong FY, Gubala V, Plaxco KW. Simultaneous Measurement of the Dissolution Kinetics of Responsive DNA Hydrogels at Multiple Length Scales. ACS NANO 2017; 11:461-468. [PMID: 28006092 DOI: 10.1021/acsnano.6b06414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recent years have seen increasing study of stimulus-responsive hydrogels constructed from aptamer-connected DNA building blocks. Presumably due to a lack of simple, quantitative tools with which to measure gel responsiveness, however, the literature describing these materials is largely qualitative. In response, we demonstrate here simple, time-resolved, multiscale methods for measuring the response kinetics of these materials. Specifically, by employing trace amounts of fluorophore-quencher labeled cross-linkers and the rheology of entrapped fluorescent particles, we simultaneously measure dissolution at molecular, hundred-nanometer, and hundred-micron length-scales. For our test-bed system, an adenine-responsive hydrogel, we find biphasic response kinetics dependent on both effector concentration and depth within the gel and a dissolution pattern uniform at scales longer than a few times the monomer-monomer distance. Likewise, we find that, in agreement with theoretical predictions, dissolution kinetics over the hundred nanometer length scale exhibit a power-law-like dependence on the fraction of disrupted cross-links before a distinct crossover from solid-like to liquid-like behavior.
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Research Support, N.I.H., Extramural |
8 |
9 |
15
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Kim EA, Panushka J, Meyer T, Ide N, Carlisle R, Baker S, Blair DF. Biogenesis of the Flagellar Switch Complex in Escherichia coli: Formation of Sub-Complexes Independently of the Basal-Body MS-Ring. J Mol Biol 2017. [PMID: 28625846 DOI: 10.1016/j.jmb.2017.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Direction switching in the flagellar motor of Escherichia coli is under the control of a complex on the rotor formed from the proteins FliG, FliM, and FliN. FliG lies at the top of the switch complex (i.e., nearest the membrane) and is arranged with its C-terminal domain (FliGC) resting on the middle domain (FliGM) of the neighboring subunit. This organization requires the protein to adopt an open conformation that exposes the surfaces engaging in intersubunit FliGC/FliGM contacts. In a recent study, Baker and coworkers [13] obtained evidence that FliG in the cytosol is monomeric and takes on a more compact conformation, with FliGC making intramolecular contact with FliGM of the same subunit. In the present work, we examine the conformational preferences and interactions of FliG through in vivo crosslinking experiments in cells that lack either all other flagellar proteins or just the MS-ring protein FliF. The results indicate that FliG has a significant tendency to form multimers independently of other flagellar components. The multimerization of FliG is promoted by FliF and also by FliM. FliM does not multimerize efficiently by itself but does so in the presence of FliG. Thus, pre-assemblies of the switch-complex proteins can form in the cytosol and might function as intermediates in assembly.
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Journal Article |
8 |
7 |
16
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Abstract
Metal shadowing of bacteria, viruses, isolated molecules, and macromolecular assemblies is another high-resolution method for observing the ultrastructure of biological specimens. The actual procedure for producing a metal shadow is relatively simple; a heavy metal is evaporated from a source at an oblique angle to the specimen. The metal atoms pile up on the surfaces that face the source, but the surfaces away from the source are shielded and receive little metal deposit, creating a "shadow." However, the process of producing biological specimens that are suitable for metal shadowing can be very complex. There are a whole host of specimen preparation techniques that can precede metal shadowing, and all provide superior preservation in comparison to air drying, a required step in negative staining procedures. The physical forces present during air drying (i.e., surface tension of the water-air interface) will literally crush most biological specimens as they dry. In this chapter I explain the development of and procedures for the production of biological specimens from macromolecular assemblies (e.g., DNA and RNA), purified isolated molecules (e.g., proteins), and isolated viruses and bacteria preparations suitable for metal shadowing. A variation on this basic technique is to rotate the specimen during the metal deposition to produce a high-resolution three-dimensional rendering of the specimen.
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chapter-article |
11 |
6 |
17
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Mathew A, Giskes F, Lekkas A, Greisch JF, Eijkel GB, Anthony IGM, Fort K, Heck AJR, Papanastasiou D, Makarov AA, Ellis SR, Heeren RMA. An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319176 DOI: 10.1021/jasms.3c00053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase.
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2 |
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18
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Habeck M. Bayesian methods in integrative structure modeling. Biol Chem 2023; 404:741-754. [PMID: 37505205 DOI: 10.1515/hsz-2023-0145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
There is a growing interest in characterizing the structure and dynamics of large biomolecular assemblies and their interactions within the cellular environment. A diverse array of experimental techniques allows us to study biomolecular systems on a variety of length and time scales. These techniques range from imaging with light, X-rays or electrons, to spectroscopic methods, cross-linking mass spectrometry and functional genomics approaches, and are complemented by AI-assisted protein structure prediction methods. A challenge is to integrate all of these data into a model of the system and its functional dynamics. This review focuses on Bayesian approaches to integrative structure modeling. We sketch the principles of Bayesian inference, highlight recent applications to integrative modeling and conclude with a discussion of current challenges and future perspectives.
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Review |
2 |
3 |
19
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Welke RW, Sperber HS, Bergmann R, Koikkarah A, Menke L, Sieben C, Krüger DH, Chiantia S, Herrmann A, Schwarzer R. Characterization of Hantavirus N Protein Intracellular Dynamics and Localization. Viruses 2022; 14:v14030457. [PMID: 35336863 PMCID: PMC8954124 DOI: 10.3390/v14030457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 02/07/2023] Open
Abstract
Hantaviruses are enveloped viruses that possess a tri-segmented, negative-sense RNA genome. The viral S-segment encodes the multifunctional nucleocapsid protein (N), which is involved in genome packaging, intracellular protein transport, immunoregulation, and several other crucial processes during hantavirus infection. In this study, we generated fluorescently tagged N protein constructs derived from Puumalavirus (PUUV), the dominant hantavirus species in Central, Northern, and Eastern Europe. We comprehensively characterized this protein in the rodent cell line CHO-K1, monitoring the dynamics of N protein complex formation and investigating co-localization with host proteins as well as the viral glycoproteins Gc and Gn. We observed formation of large, fibrillar PUUV N protein aggregates, rapidly coalescing from early punctate and spike-like assemblies. Moreover, we found significant spatial correlation of N with vimentin, actin, and P-bodies but not with microtubules. N constructs also co-localized with Gn and Gc albeit not as strongly as the glycoproteins associated with each other. Finally, we assessed oligomerization of N constructs, observing efficient and concentration-dependent multimerization, with complexes comprising more than 10 individual proteins.
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Loquet A, Tolchard J, Berbon M, Martinez D, Habenstein B. Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy. J Vis Exp 2017:55779. [PMID: 28994783 PMCID: PMC5752270 DOI: 10.3791/55779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13C/15N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.
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Pasani S, Menon KS, Viswanath S. The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling. Protein Sci 2024; 33:e5217. [PMID: 39548826 PMCID: PMC11568391 DOI: 10.1002/pro.5217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 11/18/2024]
Abstract
Desmosomes mediate cell-cell adhesion and are prevalent in tissues under mechanical stress. However, their detailed structural characterization is not available. Here, we characterized the molecular architecture of the desmosomal outer dense plaque (ODP) using Bayesian integrative structural modeling via the Integrative Modeling Platform. Starting principally from the structural interpretation of a cryo-electron tomography (cryo-ET) map of the ODP, we integrated information from x-ray crystallography, an immuno-electron microscopy study, biochemical assays, in silico predictions of transmembrane and disordered regions, homology modeling, and stereochemistry information. The integrative structure was validated by information from imaging, tomography, and biochemical studies that were not used in modeling. The ODP resembles a densely packed cylinder with a plakophilin (PKP) layer and a plakoglobin (PG) layer; the desmosomal cadherins and PKP span these two layers. Our integrative approach allowed us to localize disordered regions, such as the N-terminus of PKP and the C-terminus of PG. We refined previous protein-protein interactions between desmosomal proteins and provided possible structural hypotheses for defective cell-cell adhesion in several diseases by mapping disease-related mutations on the structure. Finally, we point to features of the structure that could confer resilience to mechanical stress. Our model provides a basis for generating experimentally verifiable hypotheses on the structure and function of desmosomal proteins in normal and disease states.
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Alonzo-Velázquez JL, Botello-Rionda S, Herrera-Guzmán R, Carrillo-Tripp M. CapsidMesh: Atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2018; 34:e2991. [PMID: 29603677 DOI: 10.1002/cnm.2991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The fundamental functions of the capsid are to protect and transport the viral genome and recognize the host cell. Descriptions of this macromolecular complex have been proposed at different scales of approximation. Here, we introduce a methodology to generate a structured volumetric mesh of icosahedral viral capsids (CapsidMesh) based on the atomic positions of their constituents. Material properties of the capsid proteins can be set on every mesh element individually. Hence, we have control over all levels of protein structure (atoms, amino acids, subunits, oligomers, and capsid). The CapsidMesh models are suitable for numerical simulations and analysis of a physical process using a third-party package. In particular, we used our methodology to generate a CapsidMesh of several capsids previously characterized by atomic force microscopy experiments and then simulated the mechanical nanoindentation through the finite element method. By fitting to the experimental linear elastic response, we estimated the elastic modulus and mechanical stresses produced on the capsids. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.
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Arvindekar S, Pathak AS, Majila K, Viswanath S. Optimizing representations for integrative structural modeling using Bayesian model selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571227. [PMID: 38168172 PMCID: PMC10760022 DOI: 10.1101/2023.12.12.571227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Motivation Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made ad hoc, manually. Results Here, we report NestOR (Nested Sampling for Optimizing Representation), a fully automated, statistically rigorous method based on Bayesian model selection to identify the optimal coarse-grained representation for a given integrative modeling setup. Given an integrative modeling setup, it determines the optimal representations from given candidate representations based on their model evidence and sampling efficiency. The performance of NestOR was evaluated on a benchmark of four macromolecular assemblies. Availability NestOR is implemented in the Integrative Modeling Platform (https://integrativemodeling.org) and is available at https://github.com/isblab/nestor.
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Xie S, Saba L, Jiang H, Bringas OR, Oghbaie M, Stefano LD, Sherman V, LaCava J. Multiparameter screen optimizes immunoprecipitation. Biotechniques 2024; 76:145-152. [PMID: 38425263 PMCID: PMC11091867 DOI: 10.2144/btn-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Immunoprecipitation (IP) coupled with mass spectrometry effectively maps protein-protein interactions when genome-wide, affinity-tagged cell collections are used. Such studies have recorded significant portions of the compositions of physiological protein complexes, providing draft 'interactomes'; yet many constituents of protein complexes still remain uncharted. This gap exists partly because high-throughput approaches cannot optimize each IP. A key challenge for IP optimization is stabilizing in vivo interactions during the transfer from cells to test tubes; failure to do so leads to the loss of genuine interactions during the IP and subsequent failure to detect. Our high-content screening method explores the relationship between in vitro chemical conditions and IP outcomes, enabling rapid empirical optimization of conditions for capturing target macromolecular assemblies.
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Pasani S, Menon KS, Viswanath S. The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.13.544884. [PMID: 37398295 PMCID: PMC10312763 DOI: 10.1101/2023.06.13.544884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Desmosomes mediate cell-cell adhesion and are prevalent in tissues under mechanical stress. However, their detailed structural characterization is not available. Here, we characterized the molecular architecture of the desmosomal outer dense plaque (ODP) using Bayesian integrative structural modeling via the Integrative Modeling Platform. Starting principally from the structural interpretation of an electron cryo-tomogram, we integrated information from X-ray crystallography, an immuno-electron microscopy study, biochemical assays, in-silico predictions of transmembrane and disordered regions, homology modeling, and stereochemistry information. The integrative structure was validated by information from imaging, tomography, and biochemical studies that were not used in modeling. The ODP resembles a densely packed cylinder with a PKP layer and a PG layer; the desmosomal cadherins and PKP span these two layers. Our integrative approach allowed us to localize disordered regions, such as N-PKP and PG-C. We refined previous protein-protein interactions between desmosomal proteins and provided possible structural hypotheses for defective cell-cell adhesion in several diseases by mapping disease-related mutations on the structure. Finally, we point to features of the structure that could confer resilience to mechanical stress. Our model provides a basis for generating experimentally verifiable hypotheses on the structure and function of desmosomal proteins in normal and disease states.
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