Iterative ACORN as a high throughput tool in structural genomics

High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available.     

Automated protein model building combined with iterative structure refinement.

In protein crystallography, much time and effort are often required to trace an initial model from an interpretable electron density map and to refine it until it best agrees with the crystallographic data. Here, we present a method to build and refine a protein model automatically and without user intervention, starting from diffraction data extending to resolution higher than 2.3 A and reasonable estimates of crystallographic phases. The method is based on an iterative procedure that describes the electron density map as a set of unconnected atoms and then searches for protein-like patterns. Automatic pattern recognition (model building) combined with refinement, allows a structural model to be obtained reliably within a few CPU hours. We demonstrate the power of the method with examples of a few recently solved structures.     

Single particle macromolecular structure determination via electron microscopy

Three-dimensional structure determination of macromolecules and macromolecular complexes is an integral part of understanding biological functions. For large protein and macromolecular complexes structure determination is often performed using electron cryomicroscopy where projection images of individual macromolecular complexes are combined to produce a three-dimensional reconstruction. Single particle methods have been devised to perform this structure determination for macromolecular complexes with little or no underlying symmetry. These computational methods generally involve an iterative process of aligning unique views of the macromolecular images followed by determination of the angular components that define those views. In this review, this structure determination process is described with the aim of clarifying a seemingly complex structural method.     

DINAMO: interactive protein alignment and model building.

MOTIVATION: To facilitate the process of structure prediction by both comparative modeling and fold recognition, we describe DINAMO, an interactive protein alignment building and model evaluation tool that dynamically couples a multiple sequence alignment editor to a molecular graphics display. DINAMO allows the user to optimize the alignment and model to satisfy the known heuristics of protein structure by means of a set of analysis tools. The analysis tools return information to both the alignment editor and graphics model in the form of visual cues (color, shape), allowing for rapid evaluation. Several analysis tools may be employed, including residue conservation, residue properties (charge, hydrophobicity, volume), residue environmental preference, and secondary structure propensity. RESULTS: We demonstrate DINAMO by building a model for submission in the 3rd annual Critical Assessment of Techniques for Protein Structure Prediction (CASP3) contest. AVAILABILITY: DINAMO is freely available as a local application or Web-based Java applet at http://tito.ucsc.edu/dinamo     

Iris: Interactive all‐in‐one graphical validation of 3D protein model iterations

Iris validation is a Python package created to represent comprehensive per‐residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third‐party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per‐chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design.     

Sequence and comparative genomic analysis of actin-related proteins

Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of approximately 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4.     

CRANK: new methods for automated macromolecular crystal structure solution

CRANK is a novel suite for automated macromolecular structure solution and uses recently developed programs for substructure detection, refinement, and phasing. CRANK utilizes methods for substructure detection and phasing and combines them with existing crystallographic programs for density modification and automated model building in a convenient and easy-to-use CCP4i graphical interface. The data model used conforms to the XML eXtensible Markup Language specification and works as a common language to communicate data between many different applications inside and outside of the suite. The application of CRANK on various test cases has yielded promising results: with minimal user input, CRANK can produce better quality solutions over currently available programs.     

Molecular evolution of ACTIN RELATED PROTEIN 6, a component of SWR1 complex in Arabidopsis

To date, it has been assumed that the evolution of a protein complex is different from that of other proteins. However, there have been few evidences to support this assumption. To understand how protein complexes evolve, we analyzed the evolutionary constraints on ACTIN RELATED PROTEIN 6 (ARP6), a component of the SWR1 complex. Interspecies complementation experiments using transgenic plants that ectopically express transARP6s (ARP6s from other organisms) showed that the function of ARP6s is conserved in plants. In addition, a yeast two-hybrid analysis revealed that this functional conservation depends on its ability to bind with both PIE1 and AtSWC6. ARP6 consists of 4 domains similar to actin. Functional analysis of chimericARP6s (domain-swapped ARP6s between Arabidopsis and mouse) demonstrated that each domain of ARP6s imposes differential evolutionary constraints. Domains 1 and 3 of ARP6 were found to interact with SWC6 and PIE1, respectively, and domain 4 provides a nuclear localization signal. Moreover, domains 1 and 3 showed a slower evolution rate than domain 4, indicating that the interacting domains have higher evolutionary constraints than non-interacting domains do. These findings suggest that the components of this protein complex have evolved coordinately to preserve their interactions.     

SANE (Structure Assisted NOE Evaluation): An automated model-based approach for NOE assignment

A reliable automated approach for assignment of NOESY spectra would allow more rapid determination of protein structures by NMR. In this paper we describe a semi-automated procedure for complete NOESY assignment (SANE, Structure Assisted NOE Evaluation), coupled to an iterative procedure for NMR structure determination where the user is directly involved. Our method is similar to ARIA [Nilges et al. (1997) J. Mol. Biol., 269, 408–422], but is compatible with the molecular dynamics suites AMBER and DYANA. The method is ideal for systems where an initial model or crystal structure is available, but has also been used successfully for ab initio structure determination. Use of this semi-automated iterative approach assists in the identification of errors in the NOE assignments to short-cut the path to an NMR solution structure.     

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting

We developed a method for structure characterization of assembly components by iterative comparative protein structure modeling and fitting into cryo-electron microscopy (cryoEM) density maps. Specifically, we calculate a comparative model of a given component by considering many alternative alignments between the target sequence and a related template structure while optimizing the fit of a model into the corresponding density map. The method relies on the previously developed Moulder protocol that iterates over alignment, model building, and model assessment. The protocol was benchmarked using 20 varied target-template pairs of known structures with less than 30% sequence identity and corresponding simulated density maps at resolutions from 5A to 25A. Relative to the models based on the best existing sequence profile alignment methods, the percentage of C(alpha) atoms that are within 5A of the corresponding C(alpha) atoms in the superposed native structure increases on average from 52% to 66%, which is half-way between the starting models and the models from the best possible alignments (82%). The test also reveals that despite the improvements in the accuracy of the fitness function, this function is still the bottleneck in reducing the remaining errors. To demonstrate the usefulness of the protocol, we applied it to the upper domain of the P8 capsid protein of rice dwarf virus that has been studied by cryoEM at 6.8A. The C(alpha) root-mean-square deviation of the model based on the remotely related template, bluetongue virus VP7, improved from 8.7A to 6.0A, while the best possible model has a C(alpha) RMSD value of 5.3A. Moreover, the resulting model fits better into the cryoEM density map than the initial template structure. The method is being implemented in our program MODELLER for protein structure modeling by satisfaction of spatial restraints and will be applicable to the rapidly increasing number of cryoEM density maps of macromolecular assemblies.     

NAPP and PIRP encode subunits of a putative wave regulatory protein complex involved in plant cell morphogenesis

The ARP2/3 complex is an important regulator of actin nucleation and branching in eukaryotic organisms. All seven subunits of the ARP2/3 complex have been identified in Arabidopsis thaliana, and mutation of at least three of the subunits results in defects in epidermal cell expansion, including distorted trichomes. However, the mechanisms regulating the activity of the ARP2/3 complex in plants are largely unknown. In mammalian cells, WAVE and WASP proteins are involved in activation of the ARP2/3 complex. WAVE1 activity is regulated by a protein complex containing NAP1/HEM/KETTE/GEX-3 and PIR121/Sra-1/CYFIP/GEX-2. Here, we show that the WAVE1 regulatory protein complex is partly conserved in plants. We have identified Arabidopsis genes encoding homologs of NAP1 (NAPP), PIR121 (PIRP), and HSPC300 (BRK1). T-DNA inactivation of NAPP and PIRP results in distorted trichomes, similar to ARP2/3 complex mutants. The napp-1 mutant is allelic to the distorted mutant gnarled. The actin cytoskeleton in napp-1 and pirp-1 mutants shows orientation defects and increased bundling compared with wild-type plants. The results presented show that activity of the ARP2/3 complex in plants is regulated through an evolutionarily conserved mechanism.     

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

MOTIVATION: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases. RESULTS: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3. AVAILABILITY: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/     

MICAL2 fine-tunes Arp2/3 for actin branching

The ARP2/3 complex promotes branched actin networks, but the importance of specific subunit isoforms is unclear. In this issue, Galloni, Carra, et al. (2021. J. Cell Biol. https://doi.org/10.1083/jcb.202102043) show that MICAL2 mediates methionine oxidation of ARP3B, thus destabilizing ARP2/3 complexes and leading to disassembly of branched actin filaments.

Remodeling of branched actin networks enables cell protrusion and sensing of the environment and is essential for cell motility. Migrating cells such as fibroblasts, immune cells, and metastatic cancer cells rely on actin dynamics to generate pushing, pulling, and squeezing forces to propel themselves. Therefore, studying the processes regulating assembly and disassembly of actin filaments is key to understanding cell locomotion in health and disease. One of the most important catalyzers of actin assembly is the Arp2/3 complex, which drives lamellipodia formation and cell protrusion. Arp2/3-generated actin networks are also important for endocytic trafficking, membrane remodeling during vesicle internalization, cargo sorting, and membrane excision (1). The seven-protein ARP2/3 complex contains two unconventional actin-related proteins (ARP2 and ARP3) and five additional subunits (ARPC1–5). Mammals express two isoforms of three of the subunits (ARP3/ARP3B, ARPC1A/ARPC1B, and ARPC5/ARPC5L), resulting in functional diversity depending on the specific isoforms incorporated into the ARP2/3 complex; however, despite some intriguing roles described in muscle development (2) and platelet function (3), little is known about the biological significance of these isoforms.The nucleation activity of ARP2/3 complex is regulated at multiple levels to ensure that new actin generation is spatially and temporally controlled. Activation is controlled by Wiskott Aldrich Syndrome Protein (WASP)–family proteins, which are themselves part of multi-protein complex machines (4). WASP-family protein complexes detect multiple inputs such as membrane phospholipids, protein–protein interactions, or post-translational modifications, and act as signaling hubs to regulate branched actin nucleation. Other proteins, such as cortactin or coronin, also modulate branch stability in an antagonistic manner (5). ARP2/3 can be post-translationally modified by phosphorylation and interaction with negative regulators, whereas actin itself is regulated by targeted oxidation of methionine residues (6). How these feedback loops that control ARP2/3 activity are coordinated with cell function is an intense area of research.Molecule interacting with CasL (MICAL) proteins have emerged as important mediators of targeted protein oxidation (6). MICAL proteins (MICAL1–3) are flavin adenine dinucleotide–binding monooxygenases capable of oxidizing target proteins (including actin), either directly or through generation of diffusible H₂O₂, which in turn oxidizes proteins in close proximity. Actin oxidation occurs on two methionine residues (Met44 and Met47), resulting in F-actin disassembly and increased cofilin-mediated F-actin severing. Although actin is the best characterized MICAL substrate, there remains the intriguing possibility of the existence of additional targets that regulate cytoskeleton dynamics.In this issue, Galloni, Carra, et al. evaluated the ability of ARP2/3 complexes, containing either ARP3 or the ARP3B isoform (i.e., isocomplexes), to promote actin assembly, and determined isoform-specific differences in their activity and molecular regulation (7). As a model system, the authors used HeLa cells infected with vaccinia virus to study actin branching, given that this virus induces actin tail nucleation in the host cells. They noticed that in cells lacking ARP3, the localization of GFP-ARP3 or GFP-ARP3B to actin tails was comparable, and both isoforms were similarly incorporated into ARP2/3 complexes (Fig. 1). However, the length of the actin tails in ARP3B-expressing cells was shorter than in ARP3-expressing counterparts. Given that ARP3 and ARP3B isocomplexes were equivalent in their ability to induce actin polymerization in vitro, these data pointed to a faster disassembly rate as the potential cause underlying shorter actin tails in ARP3B-expressing cells. Indeed, by tracking photoactivatable actin to study its dynamics, the researchers confirmed that the rate of filament disassembly was faster in ARP3B-expressing cells.Open in a separate windowFigure 1.Vaccinia virus surfs on the outside of the cell, forming an actin tail in the cytoplasm that aids its propulsion. Arp2/3 complex is involved in initiating the branched actin structures and shows slow dissociation from the branches when it is stabilized by the linker protein cortactin. When an Arp2/3 complex containing the ARP3B isoform of ARP3 forms, the dissociation is enhanced, as ARP3B is subject to oxidation by MICAL2, which is recruited to branches by coronin, causing cortactin displacement and rapid branch dissociating leading to shorter actin tails.To identify the molecular basis for the differences between ARP3 and ARP3B, the authors tested a series of ARP3 and ARP3B chimeric proteins, which revealed the importance of ARP3B amino acids 281–418 in mediating the functional differences with ARP3. In particular, Met293 was essential for ARP3B to generate short actin tails. Given that MICAL enzymes promote actin filament disassembly through oxidation of actin Met44 and Met47, Galloni, Carra, et al. decided to investigate the possibility that MICAL-induced oxidation of Met293 in ARP3B inhibits ARP3B activity. Fluorescently tagged MICAL2, but not MICAL1, was recruited to vaccinia-induced actin tails at a position relatively distant from the virus itself, similar to the actin-binding protein coronin (8). Down-regulation of MICAL2, but not MICAL1, increased actin tail stability and suppressed the short actin tail phenotype induced by ARP3B overexpression. Using an antibody raised against oxidized Met293, the researchers confirmed that ARP3B oxidation was reduced following MICAL2 knockdown. Recruitment of MICAL2 to actin tails was dependent on coronin 1C expression, and silencing of coronin 1C resulted in actin filament stabilization and reversal of ARP3B-induced actin tail shortening comparable to MICAL2 knockdown. Thus, coronin 1C recruitment of MICAL2 results in ARP3B oxidation on Met293, leading to dissociation of ARP2/3B isocomplexes and consequent actin networks destabilization.Interestingly, the authors noted that the actin nucleation promoting factor cortactin, which stabilizes ARP2/3-mediated branch points along actin filaments, was required for actin tail destabilization in ARP3B overexpressing cells but was not necessary for localization of coronin 1C or MICAL2 to actin tails. One possibility is that cortactin supports local MICAL2-mediated oxidation of ARP3B at branch points to induce filament de-branching, rather than bulk actin filament depolymerization that would result from direct actin oxidation. Since MICAL proteins are directed to specific cytoskeleton locations by interacting with Myosin 5A (9) and Myosin 15 (10), the consequences of MICAL activity on actin cytoskeleton organization and function may be fine-tuned by specific MICAL subcellular localization and interacting partners.Given that actin binds directly to the catalytic monooxygenase and calponin homology domains of MICAL proteins to increase enzyme activity and promote methionine oxidation, it is not entirely surprising that the actin-related ARP3B protein can be oxidized by MICAL2. However, the location of Met293 in ARP3B is not analogous to the Met44 or Met47 residues of actin, which raises questions regarding the mechanism of ARP3B oxidation by MICAL2. Structural modeling of the MICAL3–actin complex positions the actin loop containing Met44 and Met47 near the enzyme active site (11). ARP3B may interact with MICAL2 differently to bring Met293 close to the active site for direct oxidation, or H₂O₂ produced by MICAL2 might diffuse and oxidize highly concentrated nearby proteins. If this second possibility were true, then it is also possible that additional protein targets (e.g., coronin 1C, cortactin, additional ARP2/3 subunits) might also be oxidized on Met or Cys residues. Since the effects of MICAL1 on actin are counteracted via reduction of the oxidized Met residues by the sulfoxide reductase enzyme SelR (12), it remains to be determined if ARP3B can be similarly reactivated.     

Arabidopsis actin-related protein ARP5 in multicellular development and DNA repair

Actin-related protein 5 (ARP5) is a conserved subunit of the INO80 chromatin-remodeling complex in yeast and mammals. We have characterized the expression and subcellular distribution of Arabidopsis thaliana ARP5 and explored its role in the epigenetic control of multicellular development and DNA repair. ARP5-specific monoclonal antibodies localized ARP5 protein to the nucleoplasm of interphase cells in Arabidopsis and Nicotiana tabacum. ARP5 promoter-reporter fusions and the ARP5 protein are ubiquitously expressed. A null mutant and a severe knockdown allele produced moderately dwarfed plants with all organs smaller than the wild type. The small and slightly deformed organs such as leaves and hypocotyls were composed of small-sized cells. The ratio of leaf stomata to epidermal cells was high in the mutant, which also exhibited a delayed stomatal development compared with the wild type. Mutant plants were hypersensitive to DNA-damaging reagents including hydroxyurea, methylmethane sulfonate, and bleocin, demonstrating a role for ARP5 in DNA repair. Interestingly, the hypersensitivity phenotype of ARP5 null allele arp5-1 is stronger than the severe knockdown allele arp5-2. Moreover, a wild-type transgene fully complemented all developmental and DNA repair mutant phenotypes. Despite the common participation of both ARP4 and ARP5 in the INO80 complex, ARP4- and ARP5-deficient plants displayed only a small subset of common phenotypes and each displayed novel phenotypes, suggesting that in Arabidopsis they have both shared and unique functions.     

PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system

Chemical crosslinking‐mass spectrometry (XL‐MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL‐MS data yield inter‐residue restraints that can be compared with high‐resolution structural data. Distances greater than the crosslinker spacer‐arm can reveal lowly populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL‐MS, there are few tools to enable rapid and facile mapping of XL‐MS data onto high‐resolution structures or structural models. PyXlinkViewer is a user‐friendly plugin for PyMOL v2 that maps intra‐protein, inter‐protein, and dead‐end crosslinks onto protein structures/models and automates the calculation of inter‐residue distances for the detected crosslinks. This enables rapid visualization of XL‐MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high‐quality images for publication.     

The nuclear actin-related protein ARP6 is a pleiotropic developmental regulator required for the maintenance of FLOWERING LOCUS C expression and repression of flowering in Arabidopsis

Actin-related proteins (ARPs) are found in the nuclei of all eukaryotic cells, but their functions are generally understood only in the context of their presence in various yeast and animal chromatin-modifying complexes. Arabidopsis thaliana ARP6 is a clear homolog of other eukaryotic ARP6s, including Saccharomyces cerevisiae ARP6, which was identified as a component of the SWR1 chromatin remodeling complex. We examined the subcellular localization, expression patterns, and loss-of-function phenotypes for this protein and found that Arabidopsis ARP6 is localized to the nucleus during interphase but dispersed away from the chromosomes during cell division. ARP6 expression was observed in all vegetative tissues as well as in a subset of reproductive tissues. Null mutations in ARP6 caused numerous defects, including altered development of the leaf, inflorescence, and flower as well as reduced female fertility and early flowering in both long- and short-day photoperiods. The early flowering of arp6 mutants was associated with reduced expression of the central floral repressor gene FLOWERING LOCUS C (FLC) as well as MADS AFFECTING FLOWERING 4 (MAF4) and MAF5. In addition, arp6 mutations suppress the FLC-mediated late flowering of a FRIGIDA-expressing line, indicating that ARP6 is required for the activation of FLC expression to levels that inhibit flowering. These results indicate that ARP6 acts in the nucleus to regulate plant development, and we propose that it does so through modulation of chromatin structure and the control of gene expression.     

The Phenix software for automated determination of macromolecular structures

X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.     

EXPRESSION AND PURIFICATION OF HUMAN ARP1 PROTEIN AND RAPID PREPARATION OF POLYCLONAL ANTIBODY

Angiopoietin-related protein 1 (ARP1) is one of the antiangiogenic factors and plays an important role in endothelial cell proliferation, migration, and blood vessel network formation. Here a rapid method to prepare ARP1 polyclonal antibody in 1 month was developed. The gene of fibrinogen homology domain (FD) for ARP1 was cloned and the protein was expressed in a soluble form of MBP-FD fused protein. The MBP-FD protein was purified using amylose affinity chromatography of maltose-binding protein. Polyclonal antibodies against MBP-FD were obtained through immunization in BALB/c mice. The titer was determined by indirect enzyme-linked immunosorbent assay (ELISA), and the antibody specificity was assessed by Western blot. The full-length ARP1 protein in stable form expressed in transfected human large lung cancer cell lines NCI-H460 was detected by immunocytochemistry (ICC) analysis using ARP1 polyclonal antibodies. The result shows that the antibody possesses good specificity and sensitivity. This work provides a substantial base for the further studies of ARP1 function and associated mechanisms.

Supplemental materials are available for this article. Go to the publisher's online edition of Preparative Biochemistry and Biotechnology to view the supplemental file.     

Modeling protein structure at near atomic resolutions with Gorgon

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 ?), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.