1
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Riggi M, Torrez RM, Iwasa JH. 3D animation as a tool for integrative modeling of dynamic molecular mechanisms. Structure 2024; 32:122-130. [PMID: 38183978 PMCID: PMC10872329 DOI: 10.1016/j.str.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/01/2023] [Accepted: 12/12/2023] [Indexed: 01/08/2024]
Abstract
As the scientific community accumulates diverse data describing how molecular mechanisms occur, creating and sharing visual models that integrate the richness of this information has become increasingly important to help us explore, refine, and communicate our hypotheses. Three-dimensional (3D) animation is a powerful tool to capture dynamic hypotheses that are otherwise difficult or impossible to visualize using traditional 2D illustration techniques. This perspective discusses the current and future roles that 3D animation can play in the research sphere.
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Affiliation(s)
- Margot Riggi
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Rachel M Torrez
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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2
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Keto L, Manninen T. CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations. Neuroinformatics 2023; 21:483-500. [PMID: 37133688 PMCID: PMC10406679 DOI: 10.1007/s12021-023-09627-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.
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Affiliation(s)
- Laura Keto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Tiina Manninen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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3
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Werner E. Strategies for the Production of Molecular Animations. FRONTIERS IN BIOINFORMATICS 2022; 2:793914. [PMID: 36304328 PMCID: PMC9580893 DOI: 10.3389/fbinf.2022.793914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/14/2022] [Indexed: 09/06/2024] Open
Abstract
Molecular animations play an increasing role in scientific visualisation and science communication. They engage viewers through non-fictional, documentary type storytelling and aim at advancing the audience. Every scene of a molecular animation is to be designed to secure clarity. To achieve this, knowledge on design principles from various design fields is essential. The relevant principles help to draw attention, guide the eye, establish relationships, convey dynamics and/or trigger a reaction. The tools of general graphic design are used to compose a signature frame, those of cinematic storytelling and user interface design to choreograph the relative movement of characters and cameras. Clarity in a scientific visualisation is reached by simplification and abstraction where the choice of the adequate representation is of great importance. A large set of illustration styles is available to chose the appropriate detail level but they are constrained by the availability of experimental data. For a high-quality molecular animation, data from different sources can be integrated, even filling the structural gaps to show a complete picture of the native biological situation. For maintaining scientific authenticity it is good practice to mark use of artistic licence which ensures transparency and accountability. The design of motion requires knowledge from molecule kinetics and kinematics. With biological macromolecules, four types of motion are most relevant: thermal motion, small and large conformational changes and Brownian motion. The principles of dynamic realism should be respected as well as the circumstances given in the crowded cellular environment. Ultimately, consistent complexity is proposed as overarching principle for the production of molecular animations and should be achieved between communication objective and abstraction/simplification, audience expertise and scientific complexity, experiment and representation, characters and environment as well as structure and motion representation.
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4
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Suating P, Ernst NE, Alagbe BD, Skinner HA, Mague JT, Ashbaugh HS, Gibb BC. On the Nature of Guest Complexation in Water: Triggered Wetting-Water-Mediated Binding. J Phys Chem B 2022; 126:3150-3160. [PMID: 35438501 PMCID: PMC9059121 DOI: 10.1021/acs.jpcb.2c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/18/2022] [Indexed: 11/30/2022]
Abstract
The complexity of macromolecular surfaces means that there are still many open questions regarding how specific areas are solvated and how this might affect the complexation of guests. Contributing to the identification and classification of the different possible mechanisms of complexation events in aqueous solution, and as part of the recent SAMPL8 exercise, we report here on the synthesis and conformational properties of TEEtOA 2, a cavitand with conformationally flexible ethyl groups at its portal. Using a combination of ITC and NMR spectroscopy, we report the binding affinities of a series of carboxylates to 2 and compare it to a related cavitand TEMOA 1. Additionally, we report MD simulations revealing how the wetting of the pocket of 2 is controlled by the conformation of its rim ethyl groups and, correspondingly, a novel triggered wetting, guest complexation mechanism, whereby the approaching guest opens up the pocket of the host, inducing its wetting and ultimately allows the formation of a hydrated host-guest complex (H·G·H2O). A general classification of complexation mechanisms is also suggested.
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Affiliation(s)
- Paolo Suating
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Nicholas E. Ernst
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Busayo D. Alagbe
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Hannah A. Skinner
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Henry S. Ashbaugh
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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5
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The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models. Nat Methods 2022; 19:513-515. [PMID: 35379948 DOI: 10.1038/s41592-022-01442-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Zhang Y, Fang Q. BlenderPhotonics: an integrated open-source software environment for three-dimensional meshing and photon simulations in complex tissues. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:083014. [PMID: 35429155 PMCID: PMC9010662 DOI: 10.1117/1.jbo.27.8.083014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
SIGNIFICANCE Rapid advances in biophotonics techniques require quantitative, model-based computational approaches to obtain functional and structural information from increasingly complex and multiscaled anatomies. The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multiphysics modeling greatly impedes the clinical translation of these modalities. AIM Although the mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues using tetrahedral meshes, the generation of such domains often requires specialized meshing tools, such as Iso2Mesh. Creating a simplified and intuitive interface for tissue anatomical modeling and optical simulations is essential toward making these advanced modeling techniques broadly accessible to the user community. APPROACH We responded to the above challenge by combining the powerful, open-source three-dimensional (3D) modeling software, Blender, with state-of-the-art 3D mesh generation and MC simulation tools, utilizing the interactive graphical user interface in Blender as the front-end to allow users to create complex tissue mesh models and subsequently launch MMC light simulations. RESULTS Here, we present a tutorial to our Python-based Blender add-on-BlenderPhotonics-to interface with Iso2Mesh and MMC, which allows users to create, configure and refine complex simulation domains and run hardware-accelerated 3D light simulations with only a few clicks. We provide a comprehensive introduction to this tool and walk readers through five examples, ranging from simple shapes to sophisticated realistic tissue models. CONCLUSIONS BlenderPhotonics is user friendly and open source, and it leverages the vastly rich ecosystem of Blender. It wraps advanced modeling capabilities within an easy-to-use and interactive interface. The latest software can be downloaded at http://mcx.space/bp.
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Affiliation(s)
- Yuxuan Zhang
- Northeastern University, Department of Bioengineering, Boston, Massachusetts, United States
| | - Qianqian Fang
- Northeastern University, Department of Bioengineering, Boston, Massachusetts, United States
- Northeastern University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
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7
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Bayarri G, Hospital A, Orozco M. 3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories. Front Mol Biosci 2021; 8:726232. [PMID: 34485386 PMCID: PMC8414788 DOI: 10.3389/fmolb.2021.726232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/03/2021] [Indexed: 11/13/2022] Open
Abstract
3D Representation Sharing (3dRS) is a web-based tool designed to share biomolecular structure representations, including 4D ensembles derived from Molecular Dynamics (MD) trajectories. The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers. The web tool allows an easy upload of structures and trajectories in different formats. The 3D representation, powered by NGL viewer, offers an interactive display with smooth visualization in modern web browsers. Multiple structures can be loaded and superposed in the same scene. 1D sequences from the loaded structures are presented and linked to the 3D representation. Multiple, pre-defined 3D molecular representations are available. The powerful NGL selection syntax allows the definition of molecular regions that can be then displayed using different representations. Important descriptors such as distances or interactions can be easily added into the representation. Trajectory frames can be explored using a common video player control panel. Trajectories are efficiently stored and transferred to the NGL viewer thanks to an MDsrv-based data streaming. The server design offers all functionalities in one single web page, with a curated user experience, involving a minimum learning curve. Extended documentation is available, including a gallery with a collection of scenes. The server requires no registration and is available at https://mmb.irbbarcelona.org/3dRS.
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Affiliation(s)
- Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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8
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Ashbaugh HS, Gibb BC, Suating P. Cavitand Complexes in Aqueous Solution: Collaborative Experimental and Computational Studies of the Wetting, Assembly, and Function of Nanoscopic Bowls in Water. J Phys Chem B 2021; 125:3253-3268. [PMID: 33651614 PMCID: PMC8040017 DOI: 10.1021/acs.jpcb.0c11017] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Water is the dominant liquid on Earth. Despite this, the main focus of supramolecular chemistry research has been on binding and assembly events in organic solvents. This arose because it is more straightforward to synthesize organic-media-soluble hosts and because of the relative simplicity of organic solvents compared to water. Nature, however, relies on water as a solvent, and spurred by this fact, supramolecular chemists have recently been making forays into the aqueous domain to understand water-mediated non-covalent interactions. These studies can benefit from the substantial understanding of the hydrophobic effect and electrostatic interactions developed by physical chemists. Nearly 20 years ago, the Gibb group first synthesized a class of water-soluble host molecules, the deep-cavity cavitands, that possess non-polar pockets that readily bind non-polar moieties in aqueous solution and are capable of assembling into a wide range of complexes with distinct stoichiometries. As such, these amphipathic host species are ideal platforms for studying the role of negatively curved features on guest complexation and the structural requirements for guided assembly processes driven by the hydrophobic effect. Here we review the collaborative experimental and computational investigations between Gibb and Ashbaugh over the past 10 years exploring questions including the following: How does water wet/solvate the non-polar surfaces of non-polar pockets? How does this wetting control the binding of non-polar guests? How does wetting affect the binding of anionic species? How does the nature and size of a guest size impact the assembly of cavitand hosts into multimeric capsular complexes? What are the conformational motifs of guests packed within the confines of capsular complexes? How might the electrostatic environment engendered by hosts impact the properties and reactivity of internalized guests?
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Affiliation(s)
- Henry S. Ashbaugh
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Paolo Suating
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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9
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Visualizing protein structures - tools and trends. Biochem Soc Trans 2021; 48:499-506. [PMID: 32196545 DOI: 10.1042/bst20190621] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
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10
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Wieczór M, Hospital A, Bayarri G, Czub J, Orozco M. Molywood: streamlining the design and rendering of molecular movies. Bioinformatics 2021; 36:4660-4661. [PMID: 32573714 PMCID: PMC8476162 DOI: 10.1093/bioinformatics/btaa584] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/04/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Motivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts—particularly, in structural biology—are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust and intuitive tool that builds on the capabilities of Visual Molecular Dynamics (VMD) to automate all stages of movie rendering. Results Molywood is a Python-based script that uses an integrated workflow to give maximal flexibility in movie design. It implements the basic concepts of actions, layers, grids and concurrency and requires no programming experience to run. Availability and implementation The script is freely available on GitLab (gitlab.com/KomBioMol/molywood) and PyPI (through pip), and features an extended documentation, tutorial and gallery hosted on mmb.irbbarcelona.org/molywood.
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Affiliation(s)
- Miłosz Wieczór
- Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk 80-233, Poland.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Genis Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Jacek Czub
- Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk 80-233, Poland
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
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11
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Abstract
An unusual feature of papillomaviruses is that their genomes are packaged into virions along with host histones. Viral minichromosomes were visualized as “beads on a string” by electron microscopy in the 1970s but, to date, little is known about the posttranslational modifications of these histones. To investigate this, we analyzed the histone modifications in HPV16/18 quasivirions, wart-derived bovine papillomavirus (BPV1), and wart-derived human papillomavirus type 1 (HPV1) using quantitative mass spectrometry. The chromatin from all three virion samples had abundant posttranslational modifications (acetylation, methylation, and phosphorylation). These histone modifications were verified by acid urea polyacrylamide electrophoresis and immunoblot analysis. Compared to matched host cell controls, the virion minichromosome was enriched in histone modifications associated with active chromatin and depleted for those commonly found in repressed chromatin. We propose that the viral minichromosome acquires specific histone modifications late in infection that are coupled to the mechanisms of viral replication, late gene expression, and encapsidation. We predict that, in turn, these same modifications benefit early stages of infection by helping to evade detection, promoting localization of the viral chromosome to beneficial regions of the nucleus, and promoting early transcription and replication.
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12
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Zhang X, Xu Q, Zi Z, Liu Z, Wan C, Crisman L, Shen J, Liu X. Programmable Extracellular Vesicles for Macromolecule Delivery and Genome Modifications. Dev Cell 2020; 55:784-801.e9. [PMID: 33296682 DOI: 10.1016/j.devcel.2020.11.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/13/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
Getting large macromolecules through the plasma membrane and endosomal barriers remains a major challenge. Here, we report a generalizable method of delivering proteins and ribonucleoproteins (RNPs) to cells in vitro and mouse liver tissue in vivo with engineered ectosomes. These ectosomes, referred to as "Gectosomes," are designed to co-encapsulate vesicular stomatitis virus G protein (VSV-G) with bioactive macromolecules via split GFP complementation. We found that this method enables active cargo loading, improves the specific activity of cargo delivery, and facilitates Gectosome purification. Experimental and mathematical modeling analyses suggest that active cargo loading reduces non-specific encapsulation of cellular proteins, particularly nucleic-acid-binding proteins. Using Gectosomes that encapsulate Cre, Ago2, and SaCas9, we demonstrate their ability to execute designed modifications of endogenous genes in cell lines in vitro and mouse liver tissue in vivo, paving the way toward applications of this technology for the treatment of a wide range of human diseases.
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Affiliation(s)
- Xiaojuan Zhang
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Quanbin Xu
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Zhike Zi
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, 14195 Berlin, Germany; German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, 10589 Berlin, Germany
| | - Zeyu Liu
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Chun Wan
- Department of MCD-Biology, University of Colorado, Boulder, CO 80309, USA
| | - Lauren Crisman
- Department of MCD-Biology, University of Colorado, Boulder, CO 80309, USA
| | - Jingshi Shen
- Department of MCD-Biology, University of Colorado, Boulder, CO 80309, USA
| | - Xuedong Liu
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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13
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Ueno Y, Muraoka S, Sato T. Skeletal animation for visualizing dynamic shapes of macromolecules. J Integr Bioinform 2020. [DOI: 10.1515/jib-2018-0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractWe apply a skeletal animation technique developed for general computer graphics animation to display the dynamic shape of protein molecules. Polygon-based models for macromolecules such as atomic representations, surface models, and protein ribbon models are deformed by the motion of skeletal bones that provide coarse-grained descriptions of detailed computer graphics models. Using the animation software Blender, we developed methods to generate the skeletal bones for molecules. Our example of the superposition of normal modes demonstrates the thermal fluctuating motion obtained from normal mode analysis. The method is also applied to display the motions of protein molecules using trajectory coordinates of a molecular dynamics simulation. We found that a standard motion capture file was practical and useful for describing the motion of the molecule using available computer graphics tools.
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Affiliation(s)
- Yutaka Ueno
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Shinya Muraoka
- Graduate School of Information Science, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Tetsuo Sato
- Department of Radiological Technology, Gunma Prefectural College of Health Sciences, 323-1 Kamioki, Maebashi, Gunma 371-0052, Japan
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14
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Yeh CT, Obendorf L, Parmeggiani F. Elfin UI: A Graphical Interface for Protein Design With Modular Building Blocks. Front Bioeng Biotechnol 2020; 8:568318. [PMID: 33195130 PMCID: PMC7644802 DOI: 10.3389/fbioe.2020.568318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/02/2020] [Indexed: 02/01/2023] Open
Abstract
Molecular models have enabled understanding of biological structures and functions and allowed design of novel macro-molecules. Graphical user interfaces (GUIs) in molecular modeling are generally focused on atomic representations, but, especially for proteins, do not usually address designs of complex and large architectures, from nanometers to microns. Therefore, we have developed Elfin UI as a Blender add-on for the interactive design of large protein architectures with custom shapes. Elfin UI relies on compatible building blocks to design single- and multiple-chain protein structures. The software can be used: (1) as an interactive environment to explore building blocks combinations; and (2) as a computer aided design (CAD) tool to define target shapes that guide automated design. Elfin UI allows users to rapidly build new protein shapes, without the need to focus on amino acid sequence, and aims to make design of proteins and protein-based materials intuitive and accessible to researchers and members of the general public with limited expertise in protein engineering.
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Affiliation(s)
- Chun-Ting Yeh
- School of Chemistry and School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Leon Obendorf
- School of Chemistry and School of Biochemistry, University of Bristol, Bristol, United Kingdom.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Fabio Parmeggiani
- School of Chemistry and School of Biochemistry, University of Bristol, Bristol, United Kingdom.,Bristol Biodesign Institute and BrisSynBio, a BBSRC/EPSRC Synthetic Biology Research Centre, University of Bristol, Bristol, United Kingdom
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15
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Gulen B, Rosselin M, Fauser J, Albers MF, Pett C, Krisp C, Pogenberg V, Schlüter H, Hedberg C, Itzen A. Identification of targets of AMPylating Fic enzymes by co-substrate-mediated covalent capture. Nat Chem 2020; 12:732-739. [PMID: 32632184 DOI: 10.1038/s41557-020-0484-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/07/2020] [Indexed: 11/09/2022]
Abstract
Various pathogenic bacteria use post-translational modifications to manipulate the central components of host cell functions. Many of the enzymes released by these bacteria belong to the large Fic family, which modify targets with nucleotide monophosphates. The lack of a generic method for identifying the cellular targets of Fic family enzymes hinders investigation of their role and the effect of the post-translational modification. Here, we establish an approach that uses reactive co-substrate-linked enzymes for proteome profiling. We combine synthetic thiol-reactive nucleotide derivatives with recombinantly produced Fic enzymes containing strategically placed cysteines in their active sites to yield reactive binary probes for covalent substrate capture. The binary complexes capture their targets from cell lysates and permit subsequent identification. Furthermore, we determined the structures of low-affinity ternary enzyme-nucleotide-substrate complexes by applying a covalent-linking strategy. This approach thus allows target identification of the Fic enzymes from both bacteria and eukarya.
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Affiliation(s)
- Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marie Rosselin
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, Umeå, Sweden
| | - Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Michael F Albers
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, Umeå, Sweden
| | - Christian Pett
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, Umeå, Sweden
| | - Christoph Krisp
- Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Vivian Pogenberg
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Hartmut Schlüter
- Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Christian Hedberg
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, Umeå, Sweden.
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, Germany. .,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
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16
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Suating P, Nguyen TT, Ernst NE, Wang Y, Jordan JH, Gibb CLD, Ashbaugh HS, Gibb BC. Proximal charge effects on guest binding to a non-polar pocket. Chem Sci 2020; 11:3656-3663. [PMID: 32864079 PMCID: PMC7424593 DOI: 10.1039/c9sc06268h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/01/2020] [Indexed: 12/24/2022] Open
Abstract
Science still does not have the ability to accurately predict the affinity that ligands have for proteins. In an attempt to address this, the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind predictive challenges is a community-wide exercise aimed at advancing computational techniques as standard predictive tools in rational drug design. In each cycle, a range of biologically relevant systems of different levels of complexity are selected to test the latest modeling methods. As part of this on-going exercise, and as a step towards understanding the important factors in context dependent guest binding, we challenged the computational community to determine the affinity of a series of negatively and positively charged guests to two constitutionally isomeric cavitand hosts: octa-acid 1, and exo-octa acid 2. Our affinity determinations, combined with molecular dynamics simulations, reveal asymmetries in affinities between host-guest pairs that cannot alone be explained by simple coulombic interactions, but also point to the importance of host-water interactions. Our work reveals the key facets of molecular recognition in water, emphasizes where improvements need to be made in modelling, and shed light on the complex problem of ligand-protein binding in the aqueous realm.
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Affiliation(s)
- Paolo Suating
- Department of Chemistry , Tulane University , New Orleans , LA 70118 , USA .
| | - Thong T Nguyen
- Department of Chemistry , Tulane University , New Orleans , LA 70118 , USA .
| | - Nicholas E Ernst
- Department of Chemistry , Tulane University , New Orleans , LA 70118 , USA .
| | - Yang Wang
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , LA 70118 , USA
| | - Jacobs H Jordan
- Department of Chemistry , Tulane University , New Orleans , LA 70118 , USA .
| | - Corinne L D Gibb
- Department of Chemistry , Tulane University , New Orleans , LA 70118 , USA .
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , LA 70118 , USA
| | - Bruce C Gibb
- Department of Chemistry , Tulane University , New Orleans , LA 70118 , USA .
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17
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Kadir SR, Insall RH, Moffatt G, McGhee J, Livingstone D. Analogies in 3D molecular visualisations: development of a cell biology animation 'How cells move - a new interpretation of old data'. J Vis Commun Med 2020; 43:35-46. [PMID: 31642358 DOI: 10.1080/17453054.2019.1671814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Cell biology and imaging technology have vastly improved over the past decades, enabling scientists to dissect the inner workings of a cell. In addition to technical limits on spatial and temporal resolution, which obscure the picture at the molecular level, the sheer density and complexity of information impede clear understanding. 3D molecular visualisation has therefore blossomed as a way to translate molecular data in a more tangible form. Whilst the molecular machinery involved in cell locomotion has been extensively studied, existing narratives describing how cells generate the forces that drive movement remain unclear. Polymerisation of a protein called actin is clearly essential. The general belief in the cell migration field is that actin polymerisation's main role is to push the leading edge of the cell forwards, while the rest of the cell follows passively. The cell migration & chemotaxis group at the CRUK Beatson Institute propose an alternative hypothesis, in which actin filaments constitute cables. Motor proteins pull on these cables, causing them to behave like the treads of a tank and drive cell movement. This article describes the development of a 3D animation that uses analogical reasoning to contrast the 'tank' hypothesis for cell locomotion with the current dogma.
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Affiliation(s)
- Shereen R Kadir
- 3D Visualisation Aesthetics Lab, University of New South Wales Art and Design, Sydney, NSW, Australia
- The School of Simulation and Visualisation, Glasgow School of Art, Glasgow, UK
| | | | - Gillian Moffatt
- The School of Simulation and Visualisation, Glasgow School of Art, Glasgow, UK
| | - John McGhee
- 3D Visualisation Aesthetics Lab, University of New South Wales Art and Design, Sydney, NSW, Australia
| | - Daniel Livingstone
- The School of Simulation and Visualisation, Glasgow School of Art, Glasgow, UK
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18
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Klein T, Viola I, Groller E, Mindek P. Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2020; 26:622-632. [PMID: 31442993 DOI: 10.1109/tvcg.2019.2934612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biologists often use computer graphics to visualize structures, which due to physical limitations are not possible to image with a microscope. One example for such structures are microtubules, which are present in every eukaryotic cell. They are part of the cytoskeleton maintaining the shape of the cell and playing a key role in the cell division. In this paper, we propose a scientifically-accurate multi-scale procedural model of microtubule dynamics as a novel application scenario for procedural animation, which can generate visualizations of their overall shape, molecular structure, as well as animations of the dynamic behaviour of their growth and disassembly. The model is spanning from tens of micrometers down to atomic resolution. All the aspects of the model are driven by scientific data. The advantage over a traditional, manual animation approach is that when the underlying data change, for instance due to new evidence, the model can be recreated immediately. The procedural animation concept is presented in its generic form, with several novel extensions, facilitating an easy translation to other domains with emergent multi-scale behavior.
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19
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Martinez X, Krone M, Alharbi N, Rose AS, Laramee RS, O'Donoghue S, Baaden M, Chavent M. Molecular Graphics: Bridging Structural Biologists and Computer Scientists. Structure 2019; 27:1617-1623. [PMID: 31564470 DOI: 10.1016/j.str.2019.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/02/2019] [Accepted: 09/10/2019] [Indexed: 01/20/2023]
Abstract
Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.
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Affiliation(s)
- Xavier Martinez
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Paris, France
| | - Michael Krone
- Big Data Visual Analytics in Life Sciences, University of Tübingen, Tübingen, Germany
| | - Naif Alharbi
- Department of Computer Science, Swansea University, Swansea, Wales, United Kingdom
| | - Alexander S Rose
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, USA
| | - Robert S Laramee
- Department of Computer Science, Swansea University, Swansea, Wales, United Kingdom
| | - Sean O'Donoghue
- Garvan Institute of Medical Research, Sydney, Australia; University of New South Wales (UNSW), Sydney, Australia; CSIRO Data61, Sydney, Australia
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Paris, France
| | - Matthieu Chavent
- Institut de Pharmacologie et de Biologie Structurale IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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20
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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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21
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Goodstadt MN, Marti-Renom MA. Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning. J Mol Biol 2018; 431:1071-1087. [PMID: 30419242 DOI: 10.1016/j.jmb.2018.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023]
Abstract
Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.
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Affiliation(s)
- Mike N Goodstadt
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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22
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Gardner A, Autin L, Barbaro B, Olson AJ, Goodsell DS. CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments. IEEE COMPUTER GRAPHICS AND APPLICATIONS 2018; 38:51-66. [PMID: 30668455 PMCID: PMC6456043 DOI: 10.1109/mcg.2018.2877076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
CellPAINT allows nonexpert users to create interactive mesoscale illustrations that integrate a variety of biological data. Like popular digital painting software, scenes are created using a palette of molecular "brushes." The current release allows creation of animated scenes with an HIV virion, blood plasma, and a simplified T-cell.
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23
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Goodsell DS, Franzen MA, Herman T. From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives. J Mol Biol 2018; 430:3954-3968. [PMID: 29885327 PMCID: PMC6186495 DOI: 10.1016/j.jmb.2018.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.
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Affiliation(s)
- David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; RCSB Protein Data Bank & Center for Integrative Proteomics Research, Rutgers State University, Piscataway, NJ 08854, USA.
| | - Margaret A Franzen
- Center for BioMolecular Modeling, Milwaukee School of Engineering, Milwaukee, WI 53202, USA
| | - Tim Herman
- Center for BioMolecular Modeling, Milwaukee School of Engineering, Milwaukee, WI 53202, USA
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24
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Olson AJ. Perspectives on Structural Molecular Biology Visualization: From Past to Present. J Mol Biol 2018; 430:3997-4012. [PMID: 30009769 PMCID: PMC6186497 DOI: 10.1016/j.jmb.2018.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022]
Abstract
Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged that technology.
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Affiliation(s)
- Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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25
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Biere N, Ghaffar M, Doebbe A, Jäger D, Rothe N, Friedrich BM, Hofestädt R, Schreiber F, Kruse O, Sommer B. Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell. J Integr Bioinform 2018; 15:/j/jib.2018.15.issue-2/jib-2018-0003/jib-2018-0003.xml. [PMID: 30001212 PMCID: PMC6167046 DOI: 10.1515/jib-2018-0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/29/2018] [Indexed: 11/15/2022] Open
Abstract
The structural modeling and representation of cells is a complex task as different microscopic, spectroscopic and other information resources have to be combined to achieve a three-dimensional representation with high accuracy. Moreover, to provide an appropriate spatial representation of the cell, a stereoscopic 3D (S3D) visualization is favorable. In this work, a structural cell model is created by combining information from various light microscopic and electron microscopic images as well as from publication-related data. At the mesoscopic level each cell component is presented with special structural and visual properties; at the molecular level a cell membrane composition and the underlying modeling method are discussed; and structural information is correlated with those at the functional level (represented by simplified energy-producing metabolic pathways). The organism used as an example is the unicellular Chlamydomonas reinhardtii, which might be important in future alternative energy production processes. Based on the 3D model, an educative S3D animation was created which was shown at conferences. The complete workflow was accomplished by using the open source 3D modeling software Blender. The discussed project including the animation is available from: http://Cm5.CELLmicrocosmos.org.
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Affiliation(s)
- Niklas Biere
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld, Germany
| | - Mehmood Ghaffar
- Bio-/Medical Informatics Department, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Anja Doebbe
- Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniel Jäger
- Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nils Rothe
- Bio-/Medical Informatics Department, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Benjamin M. Friedrich
- Biological Algorithms Group, Center for Advancing Electronics Dresden, Technical University Dresden, Dresden, Germany
| | - Ralf Hofestädt
- Bio-/Medical Informatics Department, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Falk Schreiber
- Computational Life Sciences, Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Björn Sommer
- Computational Life Sciences, Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Melbourne, Australia
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26
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Bartesaghi A, Aguerrebere C, Falconieri V, Banerjee S, Earl LA, Zhu X, Grigorieff N, Milne JLS, Sapiro G, Wu X, Subramaniam S. Atomic Resolution Cryo-EM Structure of β-Galactosidase. Structure 2018; 26:848-856.e3. [PMID: 29754826 DOI: 10.1016/j.str.2018.04.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/02/2018] [Accepted: 04/05/2018] [Indexed: 01/30/2023]
Abstract
The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.
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Affiliation(s)
- Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Cecilia Aguerrebere
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Soojay Banerjee
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xing Zhu
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jacqueline L S Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Guillermo Sapiro
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Xiongwu Wu
- Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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27
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Klein T, Autin L, Kozlikova B, Goodsell DS, Olson A, Groller ME, Viola I. Instant Construction and Visualization of Crowded Biological Environments. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2018; 24:862-872. [PMID: 28866533 PMCID: PMC5746312 DOI: 10.1109/tvcg.2017.2744258] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.
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28
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Rajendiran N, Durrant JD. Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques. J Comput Chem 2017; 39:748-755. [PMID: 29280166 DOI: 10.1002/jcc.25155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/25/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023]
Abstract
Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Nivedita Rajendiran
- Department of Biological Sciences, 4200 Fifth Ave, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260
| | - Jacob D Durrant
- Department of Biological Sciences, 4200 Fifth Ave, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260
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29
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Robert-Paganin J, Halladjian M, Blaud M, Lebaron S, Delbos L, Chardon F, Capeyrou R, Humbert O, Henry Y, Henras AK, Réty S, Leulliot N. Functional link between DEAH/RHA helicase Prp43 activation and ATP base binding. Nucleic Acids Res 2017; 45:1539-1552. [PMID: 28180308 PMCID: PMC5388414 DOI: 10.1093/nar/gkw1233] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 02/05/2023] Open
Abstract
The DEAH box helicase Prp43 is a bifunctional enzyme from the DEAH/RHA helicase family required both for the maturation of ribosomes and for lariat intron release during splicing. It interacts with G-patch domain containing proteins which activate the enzymatic activity of Prp43 in vitro by an unknown mechanism. In this work, we show that the activation by G-patch domains is linked to the unique nucleotide binding mode of this helicase family. The base of the ATP molecule is stacked between two residues, R159 of the RecA1 domain (R-motif) and F357 of the RecA2 domain (F-motif). Using Prp43 F357A mutants or pyrimidine nucleotides, we show that the lack of stacking of the nucleotide base to the F-motif decouples the NTPase and helicase activities of Prp43. In contrast the R159A mutant (R-motif) showed reduced ATPase and helicase activities. We show that the Prp43 R-motif mutant induces the same phenotype as the absence of the G-patch protein Gno1, strongly suggesting that the processing defects observed in the absence of Gno1 result from a failure to activate the Prp43 helicase. Overall we propose that the stacking between the R- and F-motifs and the nucleotide base is important for the activity and regulation of this helicase family.
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Affiliation(s)
- Julien Robert-Paganin
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Maral Halladjian
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Magali Blaud
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Simon Lebaron
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Lila Delbos
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Florian Chardon
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Régine Capeyrou
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Stéphane Réty
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Nicolas Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
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30
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Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci 2017; 27:112-128. [PMID: 28836357 DOI: 10.1002/pro.3280] [Citation(s) in RCA: 1196] [Impact Index Per Article: 170.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/11/2022]
Abstract
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.
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Affiliation(s)
| | - Dave Engel
- Pacific Northwest National Laboratory, Richland, Washington
| | - Keith Star
- Pacific Northwest National Laboratory, Richland, Washington
| | - Kyle Monson
- Pacific Northwest National Laboratory, Richland, Washington
| | - Juan Brandi
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | | | - Jiahui Chen
- Southern Methodist University, Dallas, Texas
| | - Karina Liles
- Pacific Northwest National Laboratory, Richland, Washington
| | - Minju Chun
- Pacific Northwest National Laboratory, Richland, Washington
| | - Peter Li
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | - Robert Konecny
- University of California San Diego, San Diego, California
| | - David R Koes
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Weihua Geng
- Southern Methodist University, Dallas, Texas
| | | | - Guo-Wei Wei
- Michigan State University, East Lansing, Michigan
| | | | | | - Nathan A Baker
- Pacific Northwest National Laboratory, Richland, Washington.,Brown University, Providence, Rhode Island
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31
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Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S. Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. Cell 2017; 171:414-426.e12. [PMID: 28985564 DOI: 10.1016/j.cell.2017.09.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/15/2017] [Accepted: 09/06/2017] [Indexed: 01/10/2023]
Abstract
Prokaryotic cells possess CRISPR-mediated adaptive immune systems that protect them from foreign genetic elements, such as invading viruses. A central element of this immune system is an RNA-guided surveillance complex capable of targeting non-self DNA or RNA for degradation in a sequence- and site-specific manner analogous to RNA interference. Although the complexes display considerable diversity in their composition and architecture, many basic mechanisms underlying target recognition and cleavage are highly conserved. Using cryoelectron microscopy (cryo-EM), we show that the binding of target double-stranded DNA (dsDNA) to a type I-F CRISPR system yersinia (Csy) surveillance complex leads to large quaternary and tertiary structural changes in the complex that are likely necessary in the pathway leading to target dsDNA degradation by a trans-acting helicase-nuclease. Comparison of the structure of the surveillance complex before and after dsDNA binding, or in complex with three virally encoded anti-CRISPR suppressors that inhibit dsDNA binding, reveals mechanistic details underlying target recognition and inhibition.
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Affiliation(s)
- Tai Wei Guo
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hui Yang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prashant Rao
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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32
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Sisto A, Stross C, van der Kamp MW, O’Connor M, McIntosh-Smith S, Johnson GT, Hohenstein EG, Manby FR, Glowacki DR, Martinez TJ. Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. Phys Chem Chem Phys 2017; 19:14924-14936. [DOI: 10.1039/c7cp00492c] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present GPU-accelerated ab initio molecular dynamics simulations of nonadiabatic dynamics in the LH2 complex in full atomistic detail.
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Affiliation(s)
- Aaron Sisto
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
| | - Clem Stross
- School of Chemistry
- University of Bristol
- Bristol
- UK
| | | | - Michael O’Connor
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | | | - Graham T. Johnson
- California Institute for Quantitative Biosciences (QB3)
- University of California
- San Francisco
- USA
- Department of Bioengineering and Therapeutic Sciences
| | | | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | - Todd J. Martinez
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
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33
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Stone JE, Sherman WR, Schulten K. Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering. IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, WORKSHOPS AND PHD FORUM : [PROCEEDINGS]. IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, WORKSHOPS AND PHD FORUM 2016; 2016:1048-1057. [PMID: 27747138 PMCID: PMC5063251 DOI: 10.1109/ipdpsw.2016.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Immersive molecular visualization provides the viewer with intuitive perception of complex structures and spatial relationships that are of critical interest to structural biologists. The recent availability of commodity head mounted displays (HMDs) provides a compelling opportunity for widespread adoption of immersive visualization by molecular scientists, but HMDs pose additional challenges due to the need for low-latency, high-frame-rate rendering. State-of-the-art molecular dynamics simulations produce terabytes of data that can be impractical to transfer from remote supercomputers, necessitating routine use of remote visualization. Hardware-accelerated video encoding has profoundly increased frame rates and image resolution for remote visualization, however round-trip network latencies would cause simulator sickness when using HMDs. We present a novel two-phase rendering approach that overcomes network latencies with the combination of omnidirectional stereoscopic progressive ray tracing and high performance rasterization, and its implementation within VMD, a widely used molecular visualization and analysis tool. The new rendering approach enables immersive molecular visualization with rendering techniques such as shadows, ambient occlusion lighting, depth-of-field, and high quality transparency, that are particularly helpful for the study of large biomolecular complexes. We describe ray tracing algorithms that are used to optimize interactivity and quality, and we report key performance metrics of the system. The new techniques can also benefit many other application domains.
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Affiliation(s)
- John E. Stone
- Beckman Institute, University of Illinois at Urbana-Champaign,
Urbana, IL, USA
| | - William R. Sherman
- Pervasive Technology Institute, Indiana University, Bloomington,
IN, USA
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign,
Urbana, IL, USA
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34
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Abstract
Fem proteins are the essential structural proteins of various gram-positive bacteria. These are of three different types namely FemX (FmhB), FemA and FemB. Only two Fem protein crystallographic structures are available till date, one for FemA in Staphylococcus aureus and another for FemX in Weissella viridescensis. In this study, computational methods are used to evaluate interaction of FemA protein with catechin and epicatechin analogues. The interaction of FemA protein with catechin and epicatechin analogues are confirmed by binding energy and scores given by Autodock Vina and UCSF Dock docking softwares, which is followed by Lipinski filters and toxicity studies using online Lipinski server of SCFBIO and OSIRIS. Catechin gallate has been found as the best ligand for FemA protein in all aspects and it has outperformed all catechin and epicatechin isomers.
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Affiliation(s)
- Divya Singhal
- Department of Biotechnology, Thapar University, Patiala-147 004, India
| | - S Saxena
- Department of Biotechnology, Thapar University, Patiala-147 004, India
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35
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Essner JB, McCay RN, Smith Ii CJ, Cobb SM, Laber CH, Baker GA. A switchable peroxidase mimic derived from the reversible co-assembly of cytochrome c and carbon dots. J Mater Chem B 2016; 4:2163-2170. [PMID: 32263183 DOI: 10.1039/c6tb00052e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a straightforward tactic to boost the inherently low peroxidase-like activity of the heme-protein equine cytochrome c (cyt c) following its electrostatic assembly onto the carbon nanodot surface. This represents the first time that carbon nanodot interaction has been demonstrated to switch a protein into a high-performance enzyme for speeding up a reaction it was not evolved to catalyze. The dramatic enhancement in peroxidase-like activity stems in part from favorable local perturbations within the heme microenvironment of cyt c which are influenced by the chemistry presented at the carbon dot surface. That is, the observed peroxidase activity is clearly moderated by the choice of molecular precursors used to prepare the carbon dots, a choice which ultimately determines the surface charges present. An exceptional catalytic efficiency (kcat/KM) of 8.04 (±1.74) × 107 M-1 s-1 was determined for carbon dot/cyt c co-assemblies, close to the theoretical diffusion-controlled limit. Notably, the activity of the carbon dot/cyt c assembly can be switched off simply by increasing the ionic strength which results in dissociation into non-catalytic components.
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Affiliation(s)
- Jeremy B Essner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
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36
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Gulen B, Petrov AS, Okafor CD, Vander Wood D, O'Neill EB, Hud NV, Williams LD. Ribosomal small subunit domains radiate from a central core. Sci Rep 2016; 6:20885. [PMID: 26876483 PMCID: PMC4753503 DOI: 10.1038/srep20885] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/05/2016] [Indexed: 12/26/2022] Open
Abstract
The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2'OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.
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Affiliation(s)
- Burak Gulen
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
| | - C Denise Okafor
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Drew Vander Wood
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Eric B O'Neill
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
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37
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Bhabha G, Johnson GT, Schroeder CM, Vale RD. How Dynein Moves Along Microtubules. Trends Biochem Sci 2015; 41:94-105. [PMID: 26678005 DOI: 10.1016/j.tibs.2015.11.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 01/20/2023]
Abstract
Cytoplasmic dynein, a member of the AAA (ATPases Associated with diverse cellular Activities) family of proteins, drives the processive movement of numerous intracellular cargos towards the minus end of microtubules. Here, we summarize the structural and motile properties of dynein and highlight features that distinguish this motor from kinesin-1 and myosin V, two well-studied transport motors. Integrating information from recent crystal and cryoelectron microscopy structures, as well as high-resolution single-molecule studies, we also discuss models for how dynein biases its movement in one direction along a microtubule track, and present a movie that illustrates these principles.
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Affiliation(s)
- Gira Bhabha
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Graham T Johnson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA
| | - Courtney M Schroeder
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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38
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Abstract
mTOR (mechanistic target of rapamycin) functions as the central regulator for cell proliferation, growth and survival. Up-regulation of proteins regulating mTOR, as well as its downstream targets, has been reported in various cancers. This has promoted the development of anti-cancer therapies targeting mTOR, namely fungal macrolide rapamycin, a naturally occurring mTOR inhibitor, and its analogues (rapalogues). One such rapalogue, everolimus, has been approved in the clinical treatment of renal and breast cancers. Although results have demonstrated that these mTOR inhibitors are effective in attenuating cell growth of cancer cells under in vitro and in vivo conditions, subsequent sporadic response to rapalogues therapy in clinical trials has promoted researchers to look further into the complex understanding of the dynamics of mTOR regulation in the tumour environment. Limitations of these rapalogues include the sensitivity of tumour subsets to mTOR inhibition. Additionally, it is well known that rapamycin and its rapalogues mediate their effects by inhibiting mTORC (mTOR complex) 1, with limited or no effect on mTORC2 activity. The present review summarizes the pre-clinical, clinical and recent discoveries, with emphasis on the cellular and molecular effects of everolimus in cancer therapy.
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39
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Transparency in film: increasing credibility of scientific animation using citation. Nat Methods 2015; 12:293-7. [PMID: 25825832 DOI: 10.1038/nmeth.3334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Sellers MS, Hurley MM. XPairIt Docking Protocolfor peptide docking and analysis. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1025267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Iwasa JH. Bringing macromolecular machinery to life using 3D animation. Curr Opin Struct Biol 2015; 31:84-8. [DOI: 10.1016/j.sbi.2015.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
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42
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Agrochemical control of plant water use using engineered abscisic acid receptors. Nature 2015; 520:545-8. [DOI: 10.1038/nature14123] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/28/2014] [Indexed: 12/13/2022]
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43
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Johnson GT, Autin L, Al-Alusi M, Goodsell DS, Sanner MF, Olson AJ. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nat Methods 2014; 12:85-91. [PMID: 25437435 PMCID: PMC4281296 DOI: 10.1038/nmeth.3204] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 10/06/2014] [Indexed: 01/17/2023]
Abstract
cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of models and with recipes and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators, and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org.
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Affiliation(s)
- Graham T Johnson
- 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA. [3] California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California, USA
| | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Mostafa Al-Alusi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Michel F Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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44
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Ueno Y, Ito S, Konagaya A. Implementing a modeling software for animated protein-complex interactions using a physics simulation library. J Bioinform Comput Biol 2014; 12:1442003. [PMID: 25385079 DOI: 10.1142/s0219720014420037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.
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Affiliation(s)
- Yutaka Ueno
- Health Research Institute, AIST Kansai, 3-11-46 Nakouji, Amagasaki, Hyogo 661-0974, Japan , Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan
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45
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Hirst JD, Glowacki DR, Baaden M. Molecular simulations and visualization: introduction and overview. Faraday Discuss 2014; 169:9-22. [DOI: 10.1039/c4fd90024c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discuss 2014; 169:23-44. [PMID: 25253262 PMCID: PMC4569901 DOI: 10.1039/c4fd00017j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022]
Abstract
As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology.
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47
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Johnson GT, Hertig S. A guide to the visual analysis and communication of biomolecular structural data. Nat Rev Mol Cell Biol 2014; 15:690-8. [PMID: 25245078 DOI: 10.1038/nrm3874] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biologists regularly face an increasingly difficult task - to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.
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Affiliation(s)
- Graham T Johnson
- 1] California Institute for Quantitative Biosciences (QB3), University of California, San Francisco; and the Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA. [2] Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
| | - Samuel Hertig
- California Institute for Quantitative Biosciences (QB3), University of California, San Francisco; and the Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
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48
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Durrant JD, Amaro RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol 2014; 10:e1003720. [PMID: 25032790 PMCID: PMC4102414 DOI: 10.1371/journal.pcbi.1003720] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022] Open
Abstract
As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. In order to build accurate large-scale models of subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature will be essential. In the current work, we present a multi-scale utility called LipidWrapper capable of creating curved membrane models with geometries derived from various sources, both experimental and theoretical. To demonstrate its utility, we use LipidWrapper to examine an important mechanism of influenza virulence. A copy of the program can be downloaded free of charge under the terms of the open-source FreeBSD License from http://nbcr.ucsd.edu/lipidwrapper. LipidWrapper has been tested on all major computer operating systems.
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Affiliation(s)
- Jacob D. Durrant
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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49
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Abstract
We present a simple procedure for the conversion of Crystallographic Information Files (CIFs) into Virtual Reality Modelling Language (VRML2, .wrl) files, which can be used as input files for three-dimensional (3D) printing.
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Affiliation(s)
- Teng-Hao Chen
- Department of Chemistry
- University of Houston
- Houston, USA
| | - Semin Lee
- Department of Chemistry
- Indiana University
- Bloomington, USA
| | - Amar H. Flood
- Department of Chemistry
- Indiana University
- Bloomington, USA
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50
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Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol 2013; 20:1243-9. [PMID: 24077226 PMCID: PMC3823643 DOI: 10.1038/nsmb.2676] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 08/16/2013] [Indexed: 11/22/2022]
Abstract
Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, E. coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics, following a pattern of divergent evolution that is tuned by the cellular environment.
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