David Goodsell

Last updated

David S. Goodsell, is an associate professor at the Scripps Research Institute [1] and research professor at Rutgers University, New Jersey [2] (joint appointment). He is especially known for his watercolor paintings of cell interiors. [3] [4]

Contents

David S. Goodsell at the booth for the RCSB Protein Data Bank in 2013 David S. Goodsell.jpg
David S. Goodsell at the booth for the RCSB Protein Data Bank in 2013

Education

David Goodsell studied a BSc in biology and chemistry at University of California Irvine. [1] After this, he did a PhD in X-ray crystallography of DNA at the University of California Los Angeles, completed in 1987. [1] [5]

Research

Since completing his PhD he has worked as a structural biologist at the Scripps Research Institute (with a 2-year period in University of California in 1992-94). [1] His research topics have included the use of structural biology and molecular dynamic simulations to investigate symmetry in protein oligomers, protein-protein interactions and for computer-aided drug design. In particular he is a developer of AutoDock, the most widely-used program used for molecular docking. [6] His main research focus areas are HIV drug resistance and structure and function of bacterial cells. [7]

Illustration

181-CascadeAndCRISPR 1vy8.tiff
Example of individual protein: Cascade surveillance complex of the Type I CRISPR bacterial immune system from Escherichia coli (2015). The Cascade protein complex (blue) bound to the crRNA guide strand (orange). ( PDB: 4tvx )
197-Zika Virus-ZikaVirus.tif
Example of molecular landscape: Zika Virus (2016). Viruses top and left with envelope proteins (red), membrane proteins (magenta), lipid membrane (light purple), RNA genome (yellow), and capsid proteins (orange). Target host cell bottom-right with cell surface receptors (green). Blood plasma molecules (yellow).

Goodsell has developed a signature style of scientific drawing. He started painting early in his childhood but did not study art in college. [8] In graduate school, Goodsell became interested in scientific illustration while writing molecular graphics programs to visualize protein and DNA structures. [8]

Goodsell's signature style uses generally very flat shading, with strong and simple colour-schemes. [9] As is typical in medical illustration, the images are simplified representations of the subject that still retain accuracy of the important features. [10] [11] His illustrations fall broadly into two categories: individual proteins, and cellular panoramas.

His images of individual proteins are typically computer generated, cell-shaded space-filling representations of proteins, often with cut-aways to show internal binding sites and cofactors. Conversely, his illustration of cell interiors (sometimes called molecular landscapes) are hand-painted in watercolours. [12] They are typically slices through a cell with highly simplified protein structures in a flat style in order to capture overall organisation without overwhelming detail. [13] These cell interiors are often displayed at an effective 1,000,000x magnification for consistency. [14] [15] The paintings therefore share a consistent style, aiming to make interpretation easy and as intuitive as possible. [16]

His illustrations are published in the "Molecule of the Month" series by the Protein Data Bank (PDB), an archive of protein structures. [8] His illustrations are used as teaching tools, [17] in textbooks, in scientific publications, [10] and as journal cover art. [18]

Process

For individual proteins, Goodsell's illustrations are directly generated from solved protein structures deposited in the PDB using custom computer renderings that he wrote in Fortran (now released as an online illustration tool). [19]

Representations of large macromolecular complexes or crowded cellular environments require interpretation and synthesis of multiple different types of scientific imaging. [20] These include X-ray crystallography and NMR for protein components, cryo electron tomography for larger complexes, and super-res light microscopy and electron microscopy for the cellular environment. [5] [21] In these cases, the focus is on portraying the relative scales, orientations and interactions between the components. [10]

Awards and recognition

In 2022 Goodsell was the recipient of the Carl Brändén Award. [22] The award honors an outstanding protein scientist who has also made exceptional contributions in the areas of education and/or service.

Bibliography

In addition to scientific papers, Goodsell is the author of several scientific books with a focus on illustration: [10] [23]

Related Research Articles

Cell biology is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living and functioning of organisms. Cell biology is the study of the structural and functional units of cells. Cell biology encompasses both prokaryotic and eukaryotic cells and has many subtopics which may include the study of cell metabolism, cell communication, cell cycle, biochemistry, and cell composition. The study of cells is performed using several microscopy techniques, cell culture, and cell fractionation. These have allowed for and are currently being used for discoveries and research pertaining to how cells function, ultimately giving insight into understanding larger organisms. Knowing the components of cells and how cells work is fundamental to all biological sciences while also being essential for research in biomedical fields such as cancer, and other diseases. Research in cell biology is interconnected to other fields such as genetics, molecular genetics, molecular biology, medical microbiology, immunology, and cytochemistry.

<span class="mw-page-title-main">DNA</span> Molecule that carries genetic information

Deoxyribonucleic acid is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

<span class="mw-page-title-main">Reverse transcriptase</span> Enzyme which generates DNA

A reverse transcriptase (RT) is an enzyme used to convert RNA genome to DNA, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible.

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organisations.

<span class="mw-page-title-main">Reporter gene</span> Technique in molecular biology

In molecular biology, a reporter gene is a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals or plants. Such genes are called reporters because the characteristics they confer on organisms expressing them are easily identified and measured, or because they are selectable markers. Reporter genes are often used as an indication of whether a certain gene has been taken up by or expressed in the cell or organism population.

<span class="mw-page-title-main">Nucleoplasm</span> Protoplasm that permeates a cells nucleus

The nucleoplasm, also known as karyoplasm, is the type of protoplasm that makes up the cell nucleus, the most prominent organelle of the eukaryotic cell. It is enclosed by the nuclear envelope, also known as the nuclear membrane. The nucleoplasm resembles the cytoplasm of a eukaryotic cell in that it is a gel-like substance found within a membrane, although the nucleoplasm only fills out the space in the nucleus and has its own unique functions. The nucleoplasm suspends structures within the nucleus that are not membrane-bound and is responsible for maintaining the shape of the nucleus. The structures suspended in the nucleoplasm include chromosomes, various proteins, nuclear bodies, the nucleolus, nucleoporins, nucleotides, and nuclear speckles.

<span class="mw-page-title-main">Bacteriorhodopsin</span> Protein used by single-celled organisms

Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by haloarchaea, a class of the Euryarchaeota. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy.

<span class="mw-page-title-main">Viral protein</span>

The term viral protein refers to both the products of the genome of a virus and any host proteins incorporated into the viral particle. Viral proteins are grouped according to their functions, and groups of viral proteins include structural proteins, nonstructural proteins, regulatory proteins, and accessory proteins. Viruses are non-living and do not have the means to reproduce on their own, instead depending on their host cell's machinery to do this. Thus, viruses do not code for most of the proteins required for their replication and the translation of their mRNA into viral proteins, but use proteins encoded by the host cell for this purpose.

<span class="mw-page-title-main">Nucleoprotein</span> Type of protein

Nucleoproteins are proteins conjugated with nucleic acids. Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.

<span class="mw-page-title-main">SH2 domain</span> Protein domain

The SH2domain is a structurally conserved protein domain contained within the Src oncoprotein and in many other intracellular signal-transducing proteins. SH2 domains bind to phosphorylated tyrosine residues on other proteins, modifying the function or activity of the SH2-containing protein. The SH2 domain may be considered the prototypical modular protein-protein interaction domain, allowing the transmission of signals controlling a variety of cellular functions. SH2 domains are especially common in adaptor proteins that aid in the signal transduction of receptor tyrosine kinase pathways.

<span class="mw-page-title-main">Cholera toxin</span> Protein complex secreted by the bacterium Vibrio cholerae

Cholera toxin is an AB5 multimeric protein complex secreted by the bacterium Vibrio cholerae. CTX is responsible for the massive, watery diarrhea characteristic of cholera infection. It is a member of the heat-labile enterotoxin family.

Ian Andrew Wilson is the Hansen Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at the Scripps Research Institute in San Diego, California, United States.

The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.

<span class="mw-page-title-main">PBX1</span> Protein found in humans

Pre-B-cell leukemia transcription factor 1 is a protein that in humans is encoded by the PBX1 gene. The homologous protein in Drosophila is known as extradenticle, and causes changes in embryonic development.

<span class="mw-page-title-main">KIF2C</span> Protein-coding gene in the species Homo sapiens

Kinesin-like protein KIF2C is a protein that in humans is encoded by the KIF2C gene.

<span class="mw-page-title-main">Helen M. Berman</span> American chemist

Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and led the Protein Structure Initiative Structural Genomics Knowledgebase.

Biological data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.

<span class="mw-page-title-main">Bruce William Stillman</span> Australian biochemist and cancer researcher

Bruce William Stillman is a biochemist and cancer researcher who has served as the Director of Cold Spring Harbor Laboratory (CSHL) since 1994 and President since 2003. He also served as the Director of its NCI-designated Cancer Center for 25 years from 1992 to 2016. During his leadership, CSHL has been ranked as the No. 1 institution in molecular biology and genetics research by Thomson Reuters. Stillman's research focuses on how chromosomes are duplicated in human cells and in yeast Saccharomyces cerevisiae; the mechanisms that ensure accurate inheritance of genetic material from one generation to the next; and how missteps in this process lead to cancer. For his accomplishments, Stillman has received numerous awards, including the Alfred P. Sloan, Jr. Prize in 2004 and the 2010 Louisa Gross Horwitz Prize, both of which he shared with Thomas J. Kelly of Memorial Sloan-Kettering Cancer Center, as well as the 2019 Canada Gairdner International Award for biomedical research, which he shared with John Diffley.

Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.

<span class="mw-page-title-main">Erica Ollmann Saphire</span> American structural biologist, immunologist and researcher

Erica Ollmann Saphire is an American structural biologist and immunologist and a professor at the La Jolla Institute for Immunology. She investigates the structural biology of viruses that cause hemorrhagic fever such as Ebola, Sudan, Marburg, Bundibugyo, and Lassa.

References

  1. 1 2 3 4 "CV of Goodsell, David". vivo.scripps.edu. Retrieved 2019-07-11.
  2. "Profile: David Goodsell". researchwithrutgers.com. Rutgers University. Retrieved 2019-07-13.
  3. Cohen, Jon (11 April 2019). "Meet the scientist painter who turns deadly viruses into beautiful works of art". Science. doi: 10.1126/science.aax6641 .
  4. 1 2 Taylor, Michelle (2019-06-17). "The Intersection of Art and Science". Laboratory Equipment. Archived from the original on June 18, 2019. Retrieved 2019-07-11.
  5. Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria João (2006). "Protein–ligand docking: Current status and future challenges". Proteins: Structure, Function, and Bioinformatics. 65 (1): 15–26. doi:10.1002/prot.21082. ISSN   1097-0134. PMID   16862531. S2CID   21569704.
  6. Goodsell, David. "Goodsell Home Page: Science". scripps.edu. Retrieved 2019-07-20.
  7. 1 2 3 Miller, Mary K. "Interview with David Goodsell". exploratorium.edu. Exploratorium Magazine. Retrieved 3 April 2015.
  8. Zackowitz, Maggie (2016-05-28). "It's The Zika Virus In Action, Drawn By A Scientist-Artist". NPR.org.
  9. 1 2 3 4 Cohen, Jon (2019-04-11). "Meet the scientist painter who turns deadly viruses into beautiful works of art". Science.
  10. Goodsell, David S.; Franzen, Margaret A.; Herman, Tim (2018-10-19). "From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives". Journal of Molecular Biology. 430 (21): 3954–3968. doi:10.1016/j.jmb.2018.06.009. ISSN   0022-2836. PMC   6186495 . PMID   29885327.
  11. Fessenden, Marissa (2016-06-21). "This Painting Shows What It Might Look Like When Zika Infects a Cell". Smithsonian. Retrieved 2019-07-11.
  12. Augenbraun, Eliene (2016-03-22). "Turning a Killer Virus into Award-Winning Art [Video]". Scientific American Blog.
  13. Shikov, Sergei (2011). "David Goodsell: The master of mol art". www.asbmb.org. American Society for Biochemistry and Molecular Biology Today.
  14. Goodsell, David (2016-02-26). "Cellular Landscapes in Watercolor". Journal of Biocommunication. 40 (1): e6. doi: 10.5210/jbc.v40i1.6627 . ISSN   0094-2499. PMC   9138463 . PMID   36407827.
  15. Goodsell, David S. (2011). "Eukaryotic cell panorama". Biochemistry and Molecular Biology Education. 39 (2): 91–101. doi: 10.1002/bmb.20494 . ISSN   1539-3429. PMID   21445900. S2CID   37998506.
  16. Goodsell, David S.; Franzen, Margaret A.; Herman, Tim (2018-10-19). "From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives". Journal of Molecular Biology. 430 (21): 3954–3968. doi:10.1016/j.jmb.2018.06.009. ISSN   0022-2836. PMC   6186495 . PMID   29885327.
  17. Söderqvist, Thomas (2010). "Selling point: David Goodsell". Nature Medicine. 16 (9): 943. doi: 10.1038/nm0910-943 . ISSN   1078-8956. PMID   20823862. S2CID   2731570.
  18. "Non-photorealistic Biomolecular Illustration". ccsb.scripps.edu. Retrieved 2019-07-20.
  19. Calderwood, Kathleen (2016-07-08). "Finding beauty in deadly viruses". ABC Radio National. Retrieved 2019-07-11.
  20. Lally, Robin (2011-02-24). "The Art of Science". Rutgers Today.
  21. "Outreach and Education". cdn.rcsb.org. Retrieved 2024-01-08.
  22. "Author: David Goodsell". americanscientist.org. 2011-06-12. Archived from the original on 2011-06-12. Retrieved 2019-07-11.