Ribbon diagram

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Ribbon diagram of myoglobin bound to haem (sticks) and oxygen (red spheres) (PDB: 1MBO ) Myoglobin.png
Ribbon diagram of myoglobin bound to haem (sticks) and oxygen (red spheres) ( PDB: 1MBO )

Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organisation of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure, such as the balls for the oxygen atoms attached to myoglobin's active site in the adjacent figure. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and non-repetitive coils or loops as lines or thin tubes. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon. [1]

Contents

Ribbon diagrams are simple yet powerful, expressing the visual basics of a molecular structure (twist, fold and unfold). This method has successfully portrayed the overall organization of protein structures, reflecting their three-dimensional nature and allowing better understanding of these complex objects both by expert structural biologists and by other scientists, students, [2] and the general public.

Ribbon schematic of triose P isomerase monomer (hand-drawn by J. Richardson, 1981) (PDB: 1TIM ) TriosePhosphateIsomerase Ribbon pastel photo mat.png
Ribbon schematic of triose P isomerase monomer (hand-drawn by J. Richardson, 1981) ( PDB: 1TIM )

History

The first ribbon diagrams, hand-drawn by Jane S. Richardson in 1980 (influenced by earlier individual illustrations), [3] were the first schematics of 3D protein structure to be produced systematically. [3] [4] They were created to illustrate a classification of protein structures for an article in Advances in Protein Chemistry [5] (now available in annotated form on-line at Anatax). These drawings were outlined in pen on tracing paper over a printout of a trace of the atomic coordinates, and shaded with colored pencil or pastels; [6] they preserved positions, smoothed the backbone path, and incorporated small local shifts to disambiguate the visual appearance. [4] As well as the triose isomerase ribbon drawing at the right, other hand-drawn examples depicted prealbumin, flavodoxin, and Cu,Zn superoxide dismutase.

In 1982, Arthur M. Lesk and co-workers first enabled automatic generation of ribbon diagrams through a computational implementation that uses Protein Data Bank files as input. [7] This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes. Most modern graphics systems provide either B-splines or Hermite splines as a basic drawing primitive. One type of spline implementation passes through each Cα guide point, producing an exact but choppy curve. Both hand-drawn and most computer ribbons (such as those shown here) are smoothed over about four successive guide points (usually the peptide midpoint) to produce a more visually pleasing and understandable representation. To give the right radius for helical spirals while preserving smooth β-strands, the splines can be modified by offsets proportional to local curvature, as first developed by Mike Carson for his Ribbons program [8] and later adapted by other molecular graphics software, such as the open-source Mage program for kinemage graphics [9] that produced the ribbon image at top right (other examples: 1XK8 trimer and DNA polymerase).

Since their inception, and continuing in the present, ribbon diagrams have been the single most common representation of protein structure and a common choice of cover image for a journal or textbook.

Current computer programs

PyMol ribbon of the structure of the tubby protein (PDB: 1C8Z ) Tubby-1c8z-pymol.png
PyMol ribbon of the structure of the tubby protein ( PDB: 1C8Z )

One popular program used for drawing ribbon diagrams is Molscript. Molscript utilizes Hermite splines to create coordinates for coils, turns, strands and helices. The curve passes through all its control points ( atoms) guided by direction vectors. The program was built on the basis of traditional molecular graphics by Arthur M. Lesk, Karl Hardman, and John Priestle. [10] Jmol is an open-source Java-based viewer for browsing molecular structures on the web; it includes a simplified "cartoon" version of ribbons. Other graphics programs such as DeepView (example: urease) and MolMol (example: SH2 domain) also produce ribbon images. KiNG [11] is the Java-based successor to Mage (examples: α-hemolysin top view and side view).

UCSF Chimera is a powerful molecular modeling program that also includes visualizations such as ribbons, notable especially for the ability to combine them with contoured shapes from cryo-electron microscopy data. [12] PyMOL, by Warren DeLano, [13] is a popular and flexible molecular graphics program (based on Python) that operates in interactive mode and also produces presentation-quality 2D images for ribbon diagrams and many other representations.

Features

Ribbon-drawing 3-techniques v.jpg
Secondary structure [4] [5]
α-HelicesCylindrical spiral ribbons, with ribbon plane approximately following plane of peptides.
β-StrandsArrows with thickness, about one-quarter as thick as they are wide, showing direction and twist of the strand from amino to carboxy end. β-sheets are seen as unified because neighboring strands twist in unison.
Loops and miscellaneous
Nonrepetitive loopsRound ropes that are fatter in the foreground and thinner towards the back, following smoothed path of Cα trace.
Junctions between loops and helicesRound rope that gradually flattens out into a thin helical ribbon.
Other features
Polypeptide direction,

NH2 and COOH termini

Small arrows on one or both of the termini, or letters. For β-strands, the direction of the arrow is sufficient. Today, the direction of the polypeptide chain is often indicated by a colour ramp.
Disulfide bondsInterlocked SS symbol or a zigzag, like a stylized lightning stroke.
Prosthetic groups or inhibitorsStick figures, or ball & stick.
MetalsSpheres.
Shading and colourShading or colour adds dimensionality to the diagram. Generally, the features at the front are the highest in contrast and those towards the back are the lowest.

See also

Related Research Articles

<span class="mw-page-title-main">Alpha helix</span> Type of secondary structure of proteins

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence.

<span class="mw-page-title-main">Beta sheet</span> Protein structural motif

The beta sheet, (β-sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, notably Alzheimer's disease.

<span class="mw-page-title-main">Protein secondary structure</span> General three-dimensional form of local segments of proteins

Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.

<span class="mw-page-title-main">Structural bioinformatics</span> Bioinformatics subfield

Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.

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

A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins although it can also represent other types of 3-dimensional data. The kinemage system is designed to optimize ease of use, interactive performance, and the perception and communication of detailed 3D information. The kinemage information is stored in a text file, human- and machine-readable, that describes the hierarchy of display objects and their properties, and includes optional explanatory text. The kinemage format is a defined chemical MIME type of 'chemical/x-kinemage' with the file extension '.kin'.

A coiled coil is a structural motif in proteins in which 2–7 alpha-helices are coiled together like the strands of a rope. Many coiled coil-type proteins are involved in important biological functions, such as the regulation of gene expression — e.g., transcription factors. Notable examples are the oncoproteins c-Fos and c-Jun, as well as the muscle protein tropomyosin.

<span class="mw-page-title-main">Ramachandran plot</span> Visual representation of allowable protein conformations

In biochemistry, a Ramachandran plot, originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles. The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Cα-C) angle in dotted lines. Because dihedral angle values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.

<span class="mw-page-title-main">PyMOL</span> Proprietary open-sourced python biology structure tool for visualisation

PyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license, and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.

<span class="mw-page-title-main">Jmol</span> Open-source Java viewer for 3D chemical structures

Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna.

Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics.

A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.

<span class="mw-page-title-main">UCSF Chimera</span>

UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use.

This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison and structural alignment.

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

BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.

<span class="mw-page-title-main">Jane S. Richardson</span> American biophysicist

Jane Shelby Richardson is an American biophysicist best known for developing the Richardson diagram, or ribbon diagram, a method of representing the 3D structure of proteins. Ribbon diagrams have become a standard representation of protein structures that has facilitated further investigation of protein structure and function globally. With interests in astronomy, math, physics, botany, and philosophy, Richardson took an unconventional route to establishing a science career. Today Richardson is a professor in biochemistry at Duke University.

<span class="mw-page-title-main">Arthur M. Lesk</span> Molecular biologist

Arthur Mallay Lesk, is a protein science researcher, who is a professor of biochemistry and molecular biology at the Pennsylvania State University in University Park.

PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).

<span class="mw-page-title-main">Chemical shift index</span> Laboratory technique

The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location as well as the type of protein secondary structure found in proteins using only backbone chemical shift data The technique was invented by David S. Wishart in 1992 for analyzing 1Hα chemical shifts and then later extended by him in 1994 to incorporate 13C backbone shifts. The original CSI method makes use of the fact that 1Hα chemical shifts of amino acid residues in helices tends to be shifted upfield relative to their random coil values and downfield in beta strands. Similar kinds of upfield and downfield trends are also detectable in backbone 13C chemical shifts.

<span class="mw-page-title-main">Backbone-dependent rotamer library</span> Collection of data on conformations of a given proteins amino acid side chains

In biochemistry, a backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations of the amino acid side chains in proteins as a function of the backbone dihedral angles φ and ψ of the Ramachandran map. By contrast, backbone-independent rotamer libraries express the frequencies and mean dihedral angles for all side chains in proteins, regardless of the backbone conformation of each residue type. Backbone-dependent rotamer libraries have been shown to have significant advantages over backbone-independent rotamer libraries, principally when used as an energy term, by speeding up search times of side-chain packing algorithms used in protein structure prediction and protein design.

References

  1. Smith, Thomas J. (October 27, 2005). "Displaying and Analyzing Atomic Structures on the Macintosh". Danforth Plant Science Center. Archived from the original on 28 March 2002.
  2. Richardson, D. C.; Richardson, J. S. (January 2002). "Teaching Molecular 3-D Literacy". Biochemistry and Molecular Biology Education. 30 (1): 21–26. doi: 10.1002/bmb.2002.494030010005 .
  3. 1 2 Richardson, Jane S. (2000), "Early ribbon drawings of proteins", Nature Structural Biology, 7 (8): 624–625, doi:10.1038/77912, PMID   10932243, S2CID   52856546 .
  4. 1 2 3 Richardson, Jane S. (1985), Schematic Drawings of Protein Structures, Methods in Enzymology, vol. 115, pp.  359–380, doi:10.1016/0076-6879(85)15026-3, ISBN   978-0-12-182015-2, PMID   3853075 .
  5. 1 2 Richardson, Jane S. (1981), Anatomy and Taxonomy of Protein Structures, Advances in Protein Chemistry, vol. 34, pp. 167–339, doi:10.1016/S0065-3233(08)60520-3, ISBN   978-0-12-034234-1, PMID   7020376 .
  6. "Science's 'Mother of Ribbon Diagrams' celebrates 50 years at Duke". Duke Stories. 2018-10-19. Retrieved 2020-06-09.
  7. Lesk, Arthur M.; Hardman, Karl D. (1982), "Computer-Generated Schematic Diagrams of Protein Structures", Science , 216 (4545): 539–540, Bibcode:1982Sci...216..539L, doi:10.1126/science.7071602, PMID   7071602 .
  8. Carson, M.; Bugg, C. E. (1986), "Algorithm for Ribbon Models of Proteins", Journal of Molecular Graphics, 4 (2): 121–122, doi:10.1016/0263-7855(86)80010-8 .
  9. Richardson, D. C.; Richardson, J. S. (January 1992), "The kinemage: a tool for scientific communication", Protein Science, 1 (1): 3–9, doi:10.1002/pro.5560010102, PMC   2142077 , PMID   1304880
  10. MolScript v2.1: About the program
  11. Chen, V. B.; Davis, I. W.; Richardson, D. C. (2009), "KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program", Protein Science, 18 (11): 2403–2409, doi:10.1002/pro.250, PMC   2788294 , PMID   19768809
  12. Goddard, Thomas D.; Huang, Conrad C.; Ferrin, Thomas E. (2005), "Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies", Structure, 13 (3): 473–482, doi: 10.1016/j.str.2005.01.006 , PMID   15766548 .
  13. Brunger, Axel T.; Wells, James A. (2009), "Warren L. DeLano, 21 June 1972-3 November 2009", Nature Structural & Molecular Biology, 16 (12): 1202–1203, doi: 10.1038/nsmb1209-1202 , PMID   19956203 .