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4.11: Biomolecular Visualization - Conceptions and Misconceptions

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    Structure determines everything in biology and chemistry. Since you learned to represent molecules with Lewis structures, it's been drilled into you that the structure of a molecule determines its physical and chemical properties. Physical properties would include melting points, boiling point, and solubility, while chemical properties include acid/base, redox, precipitation, and general chemical reactivity determined by the presence of Lewis/Brønsted acids and bases, and nucleophiles and electrophiles. More modern analyzes of reactivity would include molecular orbital theory descriptions of bonding.

    What makes chemistry and it's fundamentally connected fields of biology and biochemistry so difficult to many is that we can't see molecules but make inferences from data (x-ray crystallography, NMR spectroscopy and cryo-EM) about the structure of a molecule (atom type, atom/bond connectivity and geometry). As the molecule get bigger (consider the muscle protein titin, also called connectin, with a molecular weight around 3.8 million) we must use computer visualization to begin to understand the structure and infer from it the resulting function and activity of the protein. As with small molecules, we can render the molecule in different ways to better understand different attributes of the molecule that confer function and activity. We ask students to view a biomolecule and infer its properties from the rendering without giving devoted attention and instruction as to how to do that.

    Small molecules

    Let's start with a small molecule like oleic acid, a long chain carboxylic acid with 18 carbon atoms and one cis (Z) double bond between carbons 9 and 10 as shown in Figure \(\PageIndex{1}\) below.

    Figure \(\PageIndex{1}\): Line drawing of oleic acid

    Table \(\PageIndex{1}\) below shows multiple ways to render the molecule. Each rendering offers insight in the function/activity of the molecule but might at the same time leave students with difficulties in interpreting them and also reinforce or install misconceptions. Each representation below shows the very same molecule. The top row shows representations without H atoms, which the bottom row shows them.

    line stick ball sphere sphere surface
    Conformer3D_CID_445639_line_NoHs.png Conformer3D_CID_445639_Stick_NoHs.png Conformer3D_CID_445639_ballstick_NoHs.png Conformer3D_CID_445639_sphere_NoHs.png Conformer3D_CID_445639_surface_NoHs.png
    Conformer3D_CID_445639_LinesHs.png Conformer3D_CID_445639_StickHs.png Conformer3D_CID_445639_BallStickHs.png Conformer3D_CID_445639_SpheresHs.png Conformer3D_CID_445639_SurfaceHs.png

    Table \(\PageIndex{1}\):Different renderings of oleic acid

    Here are some important things to remember about biomolecular structures including both small and large molecules:

    • Biomolecular models obtained through x-ray crystallography analyzes are really built by computer programs from relative electron densities in the crystal at each point in space. Based on the electron density maps and known bond lengths, bond angles, atom types and sizes, the programs calculate the structure. Most structures used in this book are found in the the Protein Data Bank. As the name implies, the structures presented are really visualized data and as such can contain mistakes (missing atoms, steric conflicts, wrong atoms), although structural refinement techniques minimize such problems.
    • Structures derived from X-ray and cryomicroscopy analyzes are static structures and represent only one of a large ensemble of possible conformational structures. As you learned from the study of simple molecules in organic chemistry, bond lengths and angles change can change within molecules. Bonds connecting two atoms can stretch, angles connecting three atoms can bend, and the torsional angle around the central single bond in a four-atom, three bond system can rotate to form eclipsed and staggered (gauche and anti) conformers.
    • PDB structures obtained by x-ray crystallography contain no H atoms as they are too small and contain too few electrons to diffract/scatter x-rays. So get used to adding them in your mind when you see a structure. This might be challenging when programs are used to calculate and show H bonds between a slightly positive H atom on a O or N atom in a protein, and another slightly negative O or N or the same or different molecule. The H bond is often shown between an N and O atoms. You must look at the atoms involved and distances between them an visualized a H atom connected to one of the. Figure \(\PageIndex{2}\) below shows an example of an H bond between two base pairs in a DNA molecule.
    Figure \(\PageIndex{2}\): Hydrogen bonds between two base pairs of DNA, with one showing actual hydrogen atoms
    • Double bonds or likely resonance structure are not typically shown in PDB structures.
    • Line, stick and ball and sticking renderings are great at showing connectivity and bond angles, but poor at showing how the size of the atoms might affect the structure and properties of the molecules. This type of information is better shown when the size of the atoms (base on their Van der Waals radii) are shown or when the surface of the molecule is determined by showing the contact surface created between the van der Waals surface of the atoms and a rolling probe (often an O atoms mimicking water).

    Large molecules

    As the molecules get larger, line, stick, and ball and stick renderings are increasing useless. New ways of visualizing structural features of the molecules become needed.The importance of multiple renderings to clarify structure/function relationships becomes clear when you wish to understand protein structure. Multiple renderings of the protein superoxide dismutase (2sod) are shown in Table \(\PageIndex{2}\) below.

    line stick cartoon sphere surface
    sod_line.png sod_stick.png sod_cartoon.png sod_spheres.png sod_surface.png

    Table \(\PageIndex{2}\): Multiple renderings of the protein superoxide dismutase

    • The same features and limitations described above for small molecule apply to large one.
    • To reveal important structural feature of the biomolecule, it is usually best to leave many atoms out and use mixed renderings with a single display of a molecule. The cartoon rendering of superoxide dismutase shows one tiny alpha helices (red) and many beta strands (yellow). All side chain and backbone atoms have been removed. The green line is the trace through the backbone of those amino acids not involve in secondary structure. The Cu and Zn ions are shown as spheres.

    Another type of surface rending, the electrostatic potential surface, is especially useful. Figure \(\PageIndex{3}\) below shows the electrostatic potential surface of superoxide dismutase taken from two different angles after simply rotating the protein.

    sod_electostaticsurace.png sod_electrostaticsurface2.png

    Figure \(\PageIndex{3}\): Electrostatic potential surface of superoxidase dismutase from two perspectives

    The red represents minimal (most negative) potential. This part of the structure would be enriched in slightly negative Os and Ns or fully negative Os (i.e. have the highest electron density). The blues represents the positive potential, centered in areas of the surface containing slight or full positive charge (i.e.the lowest electron density). This enzyme binds superoxide, O2-, which is a toxic free radical reduction product of dioxygen, \(\ce{O2}\). It catalyzes this reaction:

    \[\ce{2 O2^{-} + 2H^{+} → O2 + H2O}.\]

    The enzyme can effectively scavenge superoxide in its vicinity as the the negative superoxide is drawn into the active site with the \(\ce{Cu}\) and \(\ce{Zn}\) atoms by the positive potential surrounding the active site, enhancing the normal diffusion encounter rate of the reactant with the enzyme pocket.

    Figure \(\PageIndex{4}\) below shows an interactive iCn3D model of the electrostatic potential of superoxidase dismutase (2sod).


    NIH_NCBI_iCn3D_Banner.svg Figure \(\PageIndex{4}\): Electrostatic potential of superoxidase dismutase (2sod) (Copyright; author via source).
    Click the image for a popup or use this external link:

    4.11: Biomolecular Visualization - Conceptions and Misconceptions is shared under a not declared license and was authored, remixed, and/or curated by Henry Jakubowski.