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      Structural basis for cofilin binding and actin filament disassembly

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          Abstract

          Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin (cofilin-decorated actin filament). The actin subunit structure of cofilactin (C-form) is distinct from those of F-actin (F-form) and monomeric actin (G-form). During the transition between these three conformations, the inner domain of actin (subdomains 3 and 4) and the majority of subdomain 1 move as two separate rigid bodies. The cofilin–actin interface consists of three distinct parts. Based on the rigid body movements of actin and the three cofilin–actin interfaces, we propose models for the cooperative binding of cofilin to actin, preferential binding of cofilin to ADP-bound actin filaments and cofilin-mediated severing of actin filaments.

          Abstract

          Cofilin is a small actin-binding protein that accelerates actin turnover by disassembling actin filaments. Here the authors present the 3.8 Å cryo-EM structure of a cofilin-decorated actin filament and discuss mechanistic implications.

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          Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.

          A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are introduced. The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM.
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            Helical reconstruction in RELION

            We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.
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              The nature of the globular- to fibrous-actin transition.

              Actin plays crucial parts in cell motility through a dynamic process driven by polymerization and depolymerization, that is, the globular (G) to fibrous (F) actin transition. Although our knowledge about the actin-based cellular functions and the molecules that regulate the G- to F-actin transition is growing, the structural aspects of the transition remain enigmatic. We created a model of F-actin using X-ray fibre diffraction intensities obtained from well oriented sols of rabbit skeletal muscle F-actin to 3.3 A in the radial direction and 5.6 A along the equator. Here we show that the G- to F-actin conformational transition is a simple relative rotation of the two major domains by about 20 degrees. As a result of the domain rotation, the actin molecule in the filament is flat. The flat form is essential for the formation of stable, helical F-actin. Our F-actin structure model provides the basis for understanding actin polymerization as well as its molecular interactions with actin-binding proteins.
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                Author and article information

                Contributors
                narita.akihiro@f.mbox.nagoya-u.ac.jp
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                10 May 2018
                10 May 2018
                2018
                : 9
                : 1860
                Affiliations
                [1 ]ISNI 0000 0001 0943 978X, GRID grid.27476.30, Structural Biology Research Center, Graduate School of Science, , Nagoya University, ; Furo-cho, Chikusa-ku, Nagoya 464-8601 Japan
                [2 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Research Center for Ultra-High Voltage Electron Microscopy, , Osaka University, ; 7-1 Mihogaoka, Ibaraki, Osaka 567-0047 Japan
                [3 ]ISNI 0000 0000 9437 3801, GRID grid.420117.1, Faculty of Health and Welfare, , Tokai Gakuin University, ; Nakakirino-cyo 5-68, Kakamigahara, Gifu 504-8511 Japan
                [4 ]ISNI 0000 0004 1769 2349, GRID grid.470014.6, Toyota Physical and Chemical Research Institute, ; 41-1, Yokomichi, Nagakute, Aichi 480-1192 Japan
                [5 ]Present Address: Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394 Japan
                Article
                4290
                10.1038/s41467-018-04290-w
                5945598
                29749375
                bf1f7cc3-8dc1-4522-965d-738cd98e5967
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 26 November 2017
                : 18 April 2018
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