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Select Molecule options

These options may allow selection of the entire molecule, subcomponent molecules (for example protein vs nucleic acid), or smaller molecular components (cofactors, carbohydrates, specific nitrogenous bases or amino acids, etc) of the model presented in the Jmol window.

Selecting a molecule so that it’s name heads the menu allows alteration of its appearance in the model.

A molecule can be hidden or revealed using the adjoining checkbox. Hiding a molecule will hide all components (atoms, bonds, ribbon, etc.) of the model associated with that molecule.

Display options

Display options determine how the selected molecule will be rendered in the model. The model may include atoms, bonds, a ribbon, trace, etc, which can be individually sized using the ‘Size’ buttons. The adjoining checkboxes can be used to hide or make visible different model components.

Atoms: Atoms can be rendered as solid spheres with a uniform radius in Angstroms, which together with bonds comprise a traditional ‘ball and stick’ projection. This is normally the default view. Note about hydrogen atoms: some models show hydrogen atoms but others do not.

vdW checkbox: toggles rendering of atoms between uniform diameters and percentage of the van der Waals radius of each element. The van der Waals Radius of an atom is the calculated radius when it is adjacent to but not bonded to another atom. Since the van der Waals radius of an element is related to the size of its electron cloud, elements with greater mass will have larger van der Waals radii.

Dots: This projects an array of small dots around the surface of atoms. Dots are a useful way to show a molecular surface while not obscuring other aspects of the molecular structure, such as a ball and stick rendering. If vdW is checked, the dots are drawn as a percent of the van der Waals radius.

Bonds: Covalent bonds are generally drawn as rods between the atoms. In some models single, double and triple bonds are distinguished (but this does not occur in all models).

H-bonds: The position of hydrogen bonds is calculated by the Jmol applet. This is performed between N-H and C-O groups of proteins and between nitrogenous bases of nucleic acids. Thus, not all hydrogen bonds may be rendered in a model.

Ribbon: A ribbon-like feature that follows the backbone of DNA and proteins. For nucleic acids, a ribbon will follow the sugar-phosphate linkages, and for proteins it follows the path of peptide bonds and alpha carbons. The flattened appearance of the ribbon highlights secondary structural features, such as the alpha-helices and beta-sheets of a protein.

Trace: Like a ribbon, a Trace follows the molecular backbone, but is rope-like in appearance. A Trace shows the path of the backbone while allowing other structural features to be emphasized.

IsoSurface: IsoSurface projects a surface to a molecule as it would appear to water molecules rolling along the perimeter. This is also referred to as the Sovent-excluded or Connolly surface. Follow this link for a more complete description of the rendering of molecular surfaces.

Color by options

Atoms, Ribbons and Traces can be colored to highlight structural features. Follow this link for a more complete description of colors.

Element: Atoms will be colored according to element type. The colors of the most common elements are:

H C N O P S Fe

1o Structure: different types of amino acids and nucleotides are given a unique color (according to the Jmol ‘shapely’ color scheme).

2o Structure: This differentiates regions of protein secondary structure:

α-helix β-sheet

4o Structure: This gives a different color to each peptide subunit of a multi-subunit protein and to each strand of a nucleic acid.

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Structure of Amino Acids and Proteins

Examine the following models to explore the structure of amino acids and proteins.

1. Amino acids. The following models show several amino acids and allow you to examine shared structural features.

All amino acids share a certain structural features. The 'backbone' of the amino acid contains a central 'alpha' carbon to which is attached a side chain group that is unique to each type of amino acid. Attached to the alpha carbon is also a carboxyl group and an amino group, which will contribute to the formation of a peptide bond when amino acids are linked together in a protein.

Select an amino and then a structural component to the atoms
Glutamate. Glutamate has an acidic side chain.
Lysine. Lysine has a basic side chain
Phenylalanine. Phenylalanine has a hydrophobic side chain
Cysteine. Cysteine has a sulfur atom on its side chain, which allows it to form disulfide bonds with other cysteine amino acids.

Alpha Carbon Side chain Carboxyl GroupAmino Group

2. Peptide bonds. Within a protein, amino acids are linked together by peptide bonds.

2a. A short peptide. This short peptide contains the sequence "Alanine--Lysine--Proline--Threonine". Alanine is at the C-terminous and Theonine is at the N-terminous. Click here to show the locations of the peptide bonds. Click hereto highlight the side chains of the amino acids in green.

2b. Amyloid Precursor Protein. The protein is a major target of research in the study of Alzheimer's Disease, and plays a role in the formation of the dense aggregates of protein (called amyloid) that form in afflicted people. Click here to zoom in on one region to see the peptide bonds (colored magenta) between the amino acids.

3. Protein Primary Structure (1o). Primary structure is the sequence of amino acids found within the protein.

Collagen. Collagen is one of the primary components of connective tissue, which helps to hold the body cells and organs together. It is a long filamentous protein, and this model initially presents a short segment in a monocolor spacefill model. Click here to reproject the model as a trace along the peptide backbones, showing that collagen actually consists of three separate peptides (colored here red, green and blue), held together by hydrogen bonding. To reveal the primary structure, it is necessary to examine the amino acid sequence of one of the peptides. Click here to focus upon one peptide. Each of the peptides of collagen has a primary structure consisting of a repeatiing sequence of the amino acids '-glycine-proline-hydroxyproline-' (hydroxyproline is a chemically modified form of proline). Click here to follow this sequence along the peptide. Collagen has a relatively simple primary structure, and each of the three peptides has the same sequence.

4. Protein Secondary Structure (2o). Secondary Structure is the presence of small-scale arrangements of amino acids.

Lysozyme. Proteins often contain several to many regions of secondary structure. Lysozyme is an antibacterial enzyme present in many body secretions, such as tears and saliva. It is presented initially in a monocolor spacefill model. Click here to reproject the protein with ribbons along the peptide backbone and colored according to the type of secondary structure: red = α-helix; yellow = β-sheet ; blue = β-turn; and white is an intervening segment.

α-Helix. Regions of secondary structure are stabilized by hydrogen bonds. Beta-amyloid is a peptide fragment abnormally cleaved from a larger protein and contributes to the formation of 'amyloid plaque' in the brains of people with Alzheimer's Disease. It consists largely of a single α-helix. Click here to highlight the hydrogen bonds. Note, however, that Jmol does not show the hydrogen bonds correctly linking to the hydrogens -- a 'bug' still to be worked out.

β-Sheet. In some proteins, amino acids are arranged predominantly as β-sheets. An example shown here is a nucleoside-channel found in the membranes of the bacterium E. coli. In this projection, the surfaces of the membrane in which the protein is embedded are depicted as a layer of spheres, red and blue for the outer and inner (cytoplasmic) surfaces, respectively. Click here to highlight the hydrogen bonds that crosslink the chains of amino acids into the sheet-like arrangement which characterizes the β-Sheet.

5. Protein Tertiary Structure (3o). Tertiary Structure is the overall 3-dimensional structure of the protein, which can range from an elongated rod to a compact, globular structure.

Amyloid Precursor Protein (again). The actual 'surface' of a protein is somewhat arbitrary to define, since it exists as electron orbitals that lack a hard surface. However, modeling the electron clouds as though they were solid spheres (a spacefill model), as shown here, gives an approximate 3-D outline of the amyloid precursor protein. Another way to show the shape of a protein is by contouring the molecular surface that actually interacts with the surrounding solvent (water). Click here to show the 'solvent-accessible surface' of the amyloid precursor protein. In general, the amino acids exposed on the surface of a soluble protein are hydrophilic and interact with water, while hydrophobic amino acids are buried within.

6. Protein Quaternary Structure (4o). Quaternary Structure is the arrangement of multiple peptides (separate peptide chains) within the overall protein. Not all proteins have 4o structure, some contain a single peptide chain. At the other extreme, some complex proteins contain a dozen or more separate peptide chains. Usually, the individual peptide chains are referred to as subunits.

Hemoglobin. Hemoglobin is a classic example of a protein with 4o structure, containing 4 subunits that include two copies each of the peptides called α-globulin and β-globulin. In this projection, the four peptides are given different colors.

Cytochrome bc1. This model shows the cytochrome bc1, one of the electrontransport proteins found in the mitochondrial membrane. Its 4o structure involves ten subunits. The red surface faces the mitochondrial intermembrane space and the blue surface faces the matrix.

7. Protein Domains. Domains are a level of structure that lie somewhere between 2o and 3o Structure. These are distinguishable structural units found within a particular peptide that encompass more complexity than a single unit of secondary structure.

MHC. MHC (Major Histocompatibility Complex) proteins function in the recognition of pathogens by the immune system. The 4o structure comprises 2 peptides (colored green and blue); a small antigenic molecule is shown in spacefill model. Each of the MHC peptides consists of two domains, connected by a intervening sequence of amino acids. Only one of the domains participates in the binding of the antigenic molecule. Click here to highlight the two domains in one of the MHC peptides. Notice how they appear to be distinct structural entities yet part of the same peptide.

8. Disulfide Bonds. Along with hydrogen bonds and hydrophobic interactions, disulfide bonds help to stabilize higher levels of protein structure, and are covalent linkages between sulfur atoms of cysteine amino acids.

Insulin. Insulin is a small protein that acts as a hormone to help regulate glucose metabolism. It contains two peptides (shown here colored green and blue) that are held together by disulfide linkages. Click here to show two of the three disulfide bonds. You will see that one of the disulfide bonds links the two peptides, and the other links two cysteines within the same peptide. How might the second disulfide bond contribute to the structure of insulin?

9. Catalytic Site. The catalytic site is the place where the enzyme actually performs its chemical reaction. It consists of a small 'pocket' where the substrate can interact with amino acids that facilitate the reaction.

Hexokinase. Hexokinase adds a phosophate group to glucose, the first step of the glycolysis pathway. A glucose molecule can be seen tucked in a deep catalytic site. Click here to zoom in and examine the catalytic site more closely.

10. Coenzymes, Cofactors, and Prosthetic groups. Coenzymes, cofactors and prosthetic groups are non-protein molecules and atoms that help proteins perform their functions. Coenzymes and cofactors are usually diffusible (not permanently bound to a protein), whereas prosthetic groups are permanently bound to the protein. Coenzymes facilitate transfer of some entity between different reactions. Examples of coenzymes, include NAD and FAD (involved in electron and hydrogen transfer), coenzyme-A (a carrier of acetyl groups) and biotin (a CO2 carrier). Cofactors are usually ions of metals such as Zn, Cu, Mn, Mg, and Fe that facilitate catalysis by an enzyme (for example the glycolyic enzyme 'pyruvate kinase' requires an Mg++ to function. A classic example of a prosthetic group is heme, which binds to O2 in the hemoglobin molecule and facilitates electron transport in the cytochrome proteins of mitochondria. The following section shows more about the heme of hemoglobin.

Heme. Heme is a small iron containing molecule that helps proteins to bind to electrons or oxygen. The model shown here is hemoglobin; if you rotate the model you will see a heme group that is associated with each ofthe four peptide subunits. Click here to zoom in and examine a heme group more closely. The position of the protein is represented by a thin line that traces the peptide backbone. The iron of heme group is covalently attached to a histidine amino acid of the peptide, indicated by the arrow. Oxygen binds to the iron (orange) of the heme, subtly altering its structure and that of the associated peptide. Click to see a heme group with or without a bound oxygen. Notice the subtle difference in the shape of the heme and the peptide chain.

11. Allosteric sites. The activity of many enzymes is influenced by the binding of non-substrate molecules to regulatory sites on the protein.

Glycerol Kinase Glycerol kinase converts glycerol to glycerol-3-phosphate with a phosphate derived from ATP. Binding of fructose-bisphosphate to an allosteric site changes the conformation of the enzyme, slowing its enzymatic activity. The model shows FBP bound to its allosteric site; notice that the catalytic site for the glycerol substrate is located in a pocket deep within the enzyme.

Dept of Biology & Environmental Science



Steven R. Spilatro
© 2008

Test Your Knowledge of Amino Acid and Protein Structure

Answer the following questions and perform the following activities. Change the appearance of the models as you wish to facilitate answering questions.

Name: _______________________

Date: _______________________

Results for Amino Acid and Protein Structure Inquiry Activities

1. The first models show several amino acids. After selecting each amino acid, identify its structural parts.

Serine Aspartate Glycine Proline

a.Click here and then on the amino acid caboxyl group.

b.Click here and then on the amino acid sidechain.

c.Click here and then on the alpha-carbon.

d.Click here and then on the amino group

e. Click all of the following that apply to the sidechain:

Polar
Acidic Charged
NonPolar Basic Uncharged
Attempts: Correct:

2. This model shows the structure of a short peptide.

Click here to show the peptide.

a. This peptide contains how many amino acids:
3 5 7 9

b.Click here and then on the peptide bonds.

c.Click here and then on any of the amino acid side chains.

d.Click here and then on the carboxyl group at the C-terminus.

e.Click here and then the N-terminus amino acid.

Attempts: Correct:

3. The next models present human erythrocyte catalase projected to highlight different structural features. Identify which level of protein structure is best demonstrated with each model.

a.Ribbon along amino acid backbone colored by structure
1O 2O 3O 4O

b.Atoms at 100% van der Waals radius with a monochrome color:
1O 2O 3O 4O

c. A trace of the protein backbone with amino acids labeled:
1O 2O 3O 4O

d.Atoms colored according to different peptide chains:
1O 2O 3O 4O

e. How many peptide subunits does this protein possess?
1 2 3 4

Attempts: Correct:

4.Click here to show the next model, the succinate dehydrogenase complex from E. coli. This enzyme oxidizes succinate from the Krebs cycle; it contains several subunits and nonprotein components.

a. Recolor the model to highlight each peptide subunit.

It contains:2 4 6 8 subunits

b. Now turn off display of protein atoms and bonds to show the non-protein components. This protein contains3 4 5 6 cofactors and coenzymes. Click on each to examine and identify it.

c. Click here to show the amino acids covalently linked to the cofactor groups. Examine these amino acids; they can be identified by clicking on them. The Fe-S groups are attached to the protein most commonly through which type of amino acid?
Pro His Asp Cys

d. Through which element is this amino acid attached to the cofactors?
SulfurNitrogenHydrogen Carbon

e. Click on the group that is a 'coenzyme'-- a nonprotein organic compound that is not covalently bonded to the protein.

Attempts: Correct:

5.Click here to show an antibody protein. Antibody proteins include several subunits with well defined domains, as well as oligosaccharides and disulfide bonds.

a. Change the model to differentially color the peptide subunits (carbohydrates will appear white). It contains:1 2 small subunits and 1 2 large subunits.

b. Click here to draw a circle around the flexible 'hinge region' of the protein. Change the model (color by element and make bonds more evident) so that disulfide bonds in this region can be seen. Click on each of the disulphide bonds. In the hinge region there are 1 2 3 disulfide bonds

c. Click here to highlight one of the heavy chain peptide subunits. Change the appearance of the molecule to highlight the secondary structure (hide atoms, show ribbons, and color by secondary structure) of the peptide. The heavy chain subunit contains 2 3 4 domains, each of which consists principally of α-helices β-sheets.

d. Click here and then change the appearance of the molecule (select and zoom in on the carbohydrate, color by element, and display as a ball & stick projection) to highlight the atomic structure of the oligosaccharide. It consists of several monosaccharides, each identfiable by its ring structure. The oligosaccharide contains 3 6 912 monosaccharides. Examine the structure of the oligosaccharide carefully; is it a linear or branched polymer of monosaccharides?
Click here and then on the monosaccharide that that is connected to three other carbohydrates.

Attempts: Correct: