cartoon only # renders as "cartoon"
color structure # changes the color of the model according to its structure 2a.
spin 10 # rotates the model at a certain speed
spin off # to stop the rotationProteins
What’s on the PDB page (RSBC - Protein Data Bank)
The PDB database is the largest digital repository of proteins, currently containing almost 200,000 macromolecular structures deposited from X-ray diffraction and nuclear magnetic resonance data, and used for research and education. Access the page and see its contents.
Access the PDB page and type 1AL1 (capital or lower case) in the search field. It is also possible to render the structure in JSmol directly by typing load=1al1 in the window that opens below.
If you want a direct link try 1AL1.
Verify that the model loaded on the PDB page refers to a structure called an alpha-helix. There is a variety of information and links to access the structure information, such as the Structure summary, 3D View, Sequence tabs, and the Macromolecules, Small molecules (linkers, modified residues), or Experimental data (how the data were obtained) boxes. In Macromolecules, for example, you will see that the structure 1AL1 reveals a peptide with the sequence ELLKKLLEELKG, considering the single-letter abbreviations for amino acids. In the upper right corner, you can download the structure (Download files) in several formats, including the PDB format, which is read by Jmol and other molecular viewers. In the Experiment tab, you can identify how the data was obtained (methodology).
What’s in the PDB file
Using the PDB website, Jmol or the JSmol applet, download the 1acj.pdb file to your computer or mobile device. Open the file in a simple text editor and observe the header information (header), the compound (compnd), the source (source), the experimental data of origin (expdta), authors, review date, journal in which the structure was published, resolution, and other data.
To illustrate the model dynamically, load the file 1acj.pdb into JSmol.
Now, in the text file, observe the information contained in a large table whose first column has the term ATOM. This is the structural information of all the atoms in the compound (note that 1acj, acetylcholinesterase, has 4193 atoms in the crystal!)
Just below there is another table, this one starting with the column HETAM, and referring to the structural information of a compound formed by heteroatoms, that is, atoms that do not participate in the protein structure, such as a ligand.
In these two tables, the last column refers to the type of atom, and the penultimate column refers to the temperature factor (B-factor). This factor expresses high values (>50) when the atom is in high vibration (protein surface, for example, due to contact with the solvent) or low values, when the vibration is reduced (inside the protein, therefore). The column immediately following refers to the degree of occupancy (occupancy) of the atom in the crystal; 1.00 indicates the same conformation for the atoms, while different values indicate multiple conformations.
The three previous columns refer to the X, Y and Z coordinates of each atom, which are used for the three-dimensional construction of the structure and geometric calculations (interatomic distance, for example).
The three previous columns refer to the X, Y and Z coordinates of each atom, which are used for the three-dimensional construction of the structure and geometric calculations (interatomic distance, for example).
3D Viewers of the RCSB Page - PDB
The PDB molecule portal also has viewers for renderable models from the PDB structure file. Check this out on the RSCB-PDB home page. Type 1mbo or any other PDB identifier in the search field and go to the 3D View tab. Note that the model is rendered in three dimensions. This is an application from the PDB website itself, and its implementation is based on the Mol* viewer developed by Molstar.
On the other hand, going to the bottom right corner of the page, it is possible to observe the structure rendered by two other programs, in Select a different viewer: NGL (WebGL), and JSmol itself!
General Anatomy of a Protein
Open the Console and download the following file from the structure bank, or from the PDB page itself:
What structure is this? Domain of porcine kidney fructose-1,6-bisphosphatase complexed to a ligand (see the Console information by Jmol, or by the PDB site, or by the show file command already seen. Although it reflects only one molecule, the model does not allow distinction of peculiarities of the structure. In this sense, try the actions below for better visualization and study, pasting each line in the Console and executing one at a time.
In any protein structure in an aqueous medium, the hydrophobic amino acid residues tend to be located in the core (interior) of the protein, while the polar ones are on its surface. To test this, visualize the protein by following the code snippet below.
spacefill only; select hydrophobic; color green; select positive; color blue; select negative; color red; select aromatic; color magenta # distribute colors to amino acid classes
rotate # observe the distribution of charged and aromatic residues
slab on; slab 50 # perform a sagittal cut in the atomic orbitals (slicing, 50% in this case)
slab off # remove the slicing featureTo visualize the protein structure with different renderings, try:
backbone only; backbone 50
trace only; trace 100Protein structural hierarchy
In order to facilitate the observation and study of parts of a protein, its structure is didactically subdivided into sequences (or structures), from primary to quinquennial.
Primary structure
The primary structure or sequence of a protein is defined by the sequence of its amino acid residues, numbered from the amino terminal (-NH\(_{2}\)) to the carboxy terminal (-COOH).
To view the primary structure of the enzyme under study, type: show sequence.
Knowledge of the primary sequence of a protein allows for a wide variety of predictive structural calculations, including its molecular mass, isoelectric point (pI), polarity and amphipathicity characteristics, as well as its structural prediction in three-dimensional space.
To view the primary structure of the enzyme under study, type: show sequence.
Knowledge of the primary sequence of a protein allows for a wide variety of predictive structural calculations, including its molecular mass, isoelectric point (pI), polarity and amphipathicity characteristics, as well as its structural prediction in three-dimensional space.
Secondary structure
The secondary structure of proteins is basically formed by helices, folds (sheets) and loops. The identification of each is facilitated by the viewer, as shown above (color structure command). When the loop is formed by less than six residues and causes an abrupt change in the direction of the polypeptide chain, it constitutes a turn.
For an interactive study of the secondary structure, load the file 8cat.pdb. Since the default initial view in Jmol is ball&stick, try:
restrict protein;cartoon only; color structureThis is bovine catalase, an enzyme with hydroperoxidase activity, commonly present in red blood cells. The default representation (by definition) of the structure coloration gives yellow color to the sheets, red to the helices and white to the turns.
To confirm these structures, type:
show info # information about chains and structure 2a. in the modelThere are also other types of secondary structures besides those mentioned. To visualize them besides the standard coloring, it is necessary for the program to calculate the secondary structures by an internal algorithm called DSSP - Define Secondary Structure . To do so:
calculate structureNote that the protein model has disappeared. To view it again, type or use the arrow keys to return to the cartoon representation and structure coloring command (cartoon only; color structure).
Now you can see that, after the calculation by the secondary structure algorithm, the image has undergone changes, with new colors appearing, purple for some helices and blue for some turns. These structures have a coded identification as shown below, and displayed by the Console in each section:
H - alpha-helix
E - extended strand of a beta-sheet
T - turn with H bond
B - isolated beta-bridge residue (only two H bonds)
G - 3/10 helix
I - pi helix
S - torsion (minimum change of 70 degrees in the curvature of the structure)Folds or beta-sheets
Folds or sheets can be parallel or antiparallel, the former being more common due to the nature of the primary structure. To visualize a folded parallel, load 2pec.pdb)
Provide a convenient visualization by cartoon or rockets, and a coloring by group:
cartoon only # or rockets only
color group # or Group, or groups, or GroupsThis coloring scheme stains the protein from the amino terminal (NH\(_{2}\)-t) region in blue to the carboxyl terminal (COOH-t) region in red.
For a better understanding of the secondary structure, load the file 2lyz.pdb related to lysozyme, a glycan hydrolase. And then:
show info # observation of structures 2as.
cartoon only; color structure
calculate structure # algorithm for optimizing structures 2as.
cartoon only; color structure # just click the up arrow on the keyboard to retrieve the command line
Now...
restrict 42-60 # restricts the view of beta sheets in the protein to a certain regionNote that the selected sheet has an antiparallel direction; if it is not clear, change the rendering to:
rockets only
spin 20 # spin off to turn off
wireframe only; wireframe 50; color cpk
calculate hbonds; hbonds 0.2 # visualization of H-bonds in the structure
zoom 150The same can be done to understand the H-bonds in an alpha helix. To do so, return to the original structure and make the following changes:
Note that the structural codes have appeared in the Console and distinct colors in the image.
select all; cartoon only; color structure; zoom 0
calculate structure
cartoon only; color structure # visualization of the 2nd calculated structuresNow select a \(\alpha\)-helix. To do this, see that in the Console, the \(\alpha\)-helices are represented by H, as already explained. Choose a region containing H and restrict your observation. You can select one with the region described in the Console (for example: H : A:109_A:114), or click on the beginning and end of a helix you want in the image, checking the position of the amino acid residue in the Console. For example:
restrict 26-36 # restricts the view to a selected alpha-helix
wireframe 50; color cpk
calculate hbondsRotate the molecule and see how the side chain of the residues is distributed in the structure. An \(\alpha\)-helix has 3.6 residues per turn, and a pitch of 0.54 nm (vertical distance between two turns). Finally, observe how the H-bonds are distributed. There are also other types of helices, such as the 3/10 helix, to be explored in the next sections.
Ramachandran Diagram
In short, the Ramachandran diagram refers to a graph represented on the plane indicating the values of the potential dihedral angles for the formation of \(\alpha\)-helix, \(\beta\)-sheets and turns, and is widely used in the structural prediction of proteins. To view it, type in the Console:
load=9pap # load the model of papain, a proteolytic enzyme from papaya
plot rama # or...plot ramachandranThe chromatic representation can be interpreted in Jmol with the same color scheme as the original rendering. Thus, \(\beta\)-sheets are colored in yellow, \(\alpha\)-helices in red, and 3/10 helices in purple. Note the content of beta sheets and \(\alpha\)-helices in different quadrants, and depending on the dihedral angles \(\phi\) and \(\psi\).
Also note the scattering of white dots outside these regions. Click on some that are outside and identify the amino acid. Not by chance, there are a large number of Gly residues, probably participating in secondary structures of turns. You can generalize this visualization by display gly. And you can also check where these residues are in the three-dimensional structure of the protein by typing model 1. Now, return to the original representation:
Also note the scattering of white dots outside these regions. Click on some that are outside and identify the amino acid. Not by chance, there are a large number of Gly residues, probably participating in secondary structures of turns. You can generalize this visualization by display gly. And you can also check where these residues are in the three-dimensional structure of the protein by typing model 1. Now, return to the original representation:
plot rama;
display all;Memorize the region covered by alpha helices (red), and identify the Pro residues:
display all;
display proNote that only one residue of Pro is found in a region predicted for an alpha helix. In practice, Pro does not participate in alpha helices because it has a pyrrolidine ring in the side chain, which blocks the orientation of this structure, a steric hindrance.
Other representations of properties are also possible with Jmol, as explained in the Commands chapter, such as mass, hydrophobicity, partial charge. To illustrate a three-dimensional plot of dihedral angles as a function of residue number, for example, type:
plot properties phi psi resnoThe Proteopedia portal has a very interesting interactive link for learning about the Ramachandran Diagram called Ramachandran Plot Inspection.
Supersecondary structures
They have this name because they are located in an intermediate organization between secondary and tertiary structures. It is a combination of a few secondary structures with a specific geometric arrangement (motifs). As an initial example, load the file 1yme.pdb, referring to the enzyme carboxypeptidase.
cartoon only;color structure
restrict 61-108 # visual restriction for a supersecondary structure
backbone only; backbone 100; color grey
spin 15This structure is formed by a beta-alpha-beta unit. With a little creativity the image seems to resemble a staple. Not surprisingly, its structural definition is “hairpin”. Another hairpin presented by carboxypeptidase, in a different view, can be obtained by: restrict 201-242; rockets only; color structure.
Now restrict the image to the other supersecondary structure:
restrict 73-102; cartoon only; color structureAlthough it is inserted in a supersecondary structure alpha-beta-alpha, it is a motif, a structure that repeats itself over a large extent in proteins. In this case, the motif alpha-turn-alpha, or alpha-alpha hairpin.
Another supersecondary structure that is curious even in its name is the beta sandwich presented by the structure 1bmw.pdb. Perform the standard cartoon rendering and structure coloring, and note the reason for the name by the juxtaposition of two antiparallel beta sheets.
You can find all the secondary structures and motifs of a protein by searching for a PDB-related site: PDBSum Database. Access it, search for carboxypeptidase (1yme), choose the Protein tab, and see the wealth of carboxypeptidase secondary structures and motifs, all with links to other information and related sites on the Internet.
You can find all the secondary structures and motifs of a protein by searching for a PDB-related site: PDBSum Database. Access it, search for carboxypeptidase (1yme), choose the Protein tab, and see the wealth of carboxypeptidase secondary structures and motifs, all with links to other information and related sites on the Internet.
To interact with the Jmol loaded with the carboxypeptidase above, select the beta hairpin structure in the PDB Sum site by clicking on its link in the Protein tab. The opened window informs you that this beta hairpin} goes from residue Val33 to Arg40. Well, identify it by selecting it in Jmol, first marking the protein with a wireframe representation. Tip: copy and paste the code snippet below into the Jmol/JSmol Console. Separating the commands with semicolons in successive lines simulates the Script Editor in the Console itself.
select all;
backbone only;
color grey;
select 33-40;
wireframe only;
wireframe 50;
color magentaFor another supersecondary structure, now load the file 1kt7.pdb, retinol-binding protein. Visualize it as usual in cartoon. Rotate the structure. The yellow section comprises the supersecondary structure called beta-barrel.
Similarly, there is also the alpha-barrel. To visualize it, load the model 3lay.pdb, a sequence of the zinc-binding protein in salmonella. Try the default rendering (structure and coloring) and rotate the molecule.
Similarly, there is also the alpha-barrel. To visualize it, load the model 3lay.pdb, a sequence of the zinc-binding protein in salmonella. Try the default rendering (structure and coloring) and rotate the molecule.
Another very common supersecondary structure that interacts with nucleic acid clefts is called a helix-turn-helix. An example can be found in the DNA-binding protein domain of the lac repressor, 1lcc.pdb. Load the structure, provide a suitable visualization, and see how it interacts with the DNA molecule.
Several other supersecondary structures can occur in proteins, such as the zinc finger, the leucine zipper, the EF hand, and the greek key.
The zinc finger and leucine zipper are commonly found interacting with DNA. Try loading 1aay.pdb and typing or copying/pasting the following sequence:
cartoon only;
color structure;
select hetero and not solvent;
spacefill 300;
color cpkJust to get an idea of the leucine zipper, , load 1ysa.pdb and type:
cartoon only;
color structure;
select leu;
spacefill 300;
color cpk
select positive;
wireframe 100;
color lightblueIn addition to the amphipathic nature of the helices, their interaction with DNA occurs through positive residues in view of the acidic nature of the double strand.
In turn, the so-called EF hand is a motif commonly found in calcium ion-binding proteins, such as calmodulin, 1cll.pdb. Load the structure, provide the usual visualization and type:
select hetero and not solvent;
spacefill 300;
color cpkBy clicking on a green sphere, its identification, a calcium atom, appears in the Console. To highlight the motif, type:
select 117-147;
color whiteAs you may have noticed, this motif is similar to the helix-turn-helix motif, but it is distinguished from it by being specific for calcium binding.
The Greek key, another supersecondary structure, comprises an arrangement of antiparallel strands, and can be visualized in 1a2t.pdb, a nuclease from staphylococcus. It is a little difficult to observe, so a more specific staining is necessary, as follows:
The Greek key, another supersecondary structure, comprises an arrangement of antiparallel strands, and can be visualized in 1a2t.pdb, a nuclease from staphylococcus. It is a little difficult to observe, so a more specific staining is necessary, as follows:
(perform it after the usual visualization):
select all;
cartoon only;
color structure;
select 7-19;
color red;
select 21-28;
color red;
select 29-36;
color green;
select 71-77;
color blueNote that the first and second strands in red are in an antiparallel arrangement to each other. The third strand in green is antiparallel to the first (red) strand, outlining the Greek key. The metaphorical drawing of a Greek key, however, is best compared to its two-dimensional structure found in textbooks.
Tertiary Structure
The tertiary structure is composed of a single polypeptide chain in a three-dimensional arrangement. Although there are a virtually infinite number of possibilities for these arrangements, proteins are sometimes classified into groups with common functional or structural similarity, and even phylogenetic similarity.
Conservation
To get an idea of the tertiary structural conservation of proteins, download the structure of the electron transport protein cytochrome c, and from 3 sources: fish, rice, and baker’s yeast. In this case, since these are files loaded from physical media, it is necessary to perform their download in advance in the program’s root directory (or in the one made root, by the command cd ?.
# Downloading the structures:
load=5cyt.pdb;write 5cyt.pdb
load=1ccr.pdb;write 1ccr.pdb
load=1ycc.pdb;write 1ycc.pdb
# Loading the models
load files "5cyt.pdb" "1ccr.pdb" "1ycc.pdb"
# Representation of the three structures with different colors and on the same screen:
frame* # all models on the same screen
select all;
trace only;
select 1.1; color white; # cit. c de peixe
select 2.1; color green; # cit. c de arroz
select 3.1; color blue # cit. c de yeastRotate the structures and see their conservation in different phyla.
Having trouble understanding conservation? Jmol allows an animation of the molecules, useful for structural alignment. To do so, type or copy/paste into the Console:
Having trouble understanding conservation? Jmol allows an animation of the molecules, useful for structural alignment. To do so, type or copy/paste into the Console:
compare {1.1} {2.1} rotate translate 2; # conjugate rotation and translation between cit. c of fish and rice
compare {3.1} {2.1} rotate translate 2; # conjugate rotation and translation between cit. c of yeast and rice
reset # center the models
zoomto 0.5 *1.5 # increase the size of the models progressively to 50% more, and at a rate of 0.5s at a time
spin 15 # rotation
delay 10; # 20s waiting time
spin off # turn off the rotationIf you got this far by running the two code snippets above, congratulations! You have just “run” scripts that automate structural observation and analysis, a great advantage of Jmol.
Conformational stability
Proteins can be classified as globular and fibrous. To study a globular protein, load papain, 9pap.pdb. Omit the solvent visualization and visualize it as wireframe, and rotate the model:
restrict protein;
wireframe only; wireframe 50
spin on # to stop, "spin off"How many amino acid residues does papain have and what is its primary sequence?
show sequence
# shows sequence 1a.
show info # shows sequence 2a.How can a protein stabilize itself conformationally? By covalent forces and weak forces. The first ones reside in the peptide bond present in the structure, in number of n-1 amino acid residues, as well as in the proximity of two thiol groups of Cys residues, forming disulfide bonds. These bonds are represented in yellow in the structure, but can be highlighted by typing or pasting the following code snippet:
trace only;
ssbonds on;
set ssbonds backbone;
ssbonds 100To visualize the residues involved in the bond as well as the remaining free thiols, select only Cys. In papain, all Cys are involved in the formation of the disulfide bond:
ssbonds off;
select cys;
wireframe 100;
color cpkNow visualize the hydrogen bonds contained in the structure:
restrict protein;
trace only; calculate hbonds
set hbonds backbone # allows you to associate H-bonds to the carbon skeleton (alternative: "set hbonds sidechain)If you manually rotate the molecule you will also notice a distribution of H-bonds between beta sheets and alpha helices of the protein’s secondary structure. To turn off H-bonds: hbonds off.
Since every atom interacts with another by dispersion forces or electronic delocalization (van der Waals and London), try visualizing the van der Waals clouds with:
dots on # "dots off" to remove the VDW surfaceElectrostatic interactions also contribute to protein stabilization, as can be seen by typing:
trace 10;
select charged;
wireframe 50;
color yellowBy rotating the structure, observe that these charged residues are located more on the surface of the protein. Identify the opposite charges of these residues, as well as those of a hydrophobic nature by:
select positive;color blue;select negative; color red # acidic and basic residues
select aromatic; wireframe 50; color green # hydrophobic residuesThe hydrophobic effect (or hydrophobic interaction) participates as a complementary weak force for the native conformation of the protein, as can be initially observed by the positioning of the aromatic residues identified in the model. Generalizing to all hydrophobic residues, it is possible to perceive their massive contribution to the stability of the protein. It is also possible to discern the aromatic residues among the hydrophobic ones:
select trp;color magenta;select phe; color pink;select tyr;color aquamarineNote that while phenolic Tyr interacts with the solvent, indolic Trp remains mainly in the protein core. :
The conformational stability of a protein is therefore dictated by strong and weak forces between its atoms and the solvent, in a three-dimensional arrangement that depends on the rotations allowed around each amino acid residue. By analyzing the dihedral angles phi and psi around the peptide bond (see the chapter on Peptides), it is possible to predict the tertiary structure based on the primary structure of the molecule. More precisely, however, it is possible to predict the secondary structure, as represented by the Ramachandran diagram.
Prosthetic groups
Several proteins depend functionally on organic structures of different origin from amino acids, the prosthetic groups (apoprotein+prosthetic group = holoprotein). For example, load the respiratory pigment myoglobin, 1mbo.pdb. –>
Disappear with the solvent, represent it as a trace and highlight the prosthetic group. To identify the latter, it is necessary to know which group it belongs to in the model: show groups. In this case, the group appears named as hem.
restrict protein;
trace only;
trace 30;
select hem;
wireframe 100; color cpk
spin 20;
delay 10;
spin offThe prosthetic group of myoglobin (and also of hemoglobin and some cytochromes) configures a porphyrin ring or heme group) formed by the juxtaposition of four pyrrole rings, with the Fe atom as the central one for the interaction with molecular oxygen. To highlight this oxygen, look for the group to which it belongs, as done above.
select oxy;spacefill 200Isolate the heme group of the protein with molecular oxygen, bring it closer, and
observe its structure next to the \(O_{2}\) molecule.
restrict (hem,oxy) and not protein;
zoom 0Note how the structure of the heme group coordinated with oxygen is planar. This is due to the binding of O\(_{2}\) with the Fe(III) of the metmyoglobin porphyrin, resulting in Fe(II)-O\(_{2}\), and converging the slightly curved conformation of the ring to planar.
Fibrous proteins
Another large group alongside globular proteins is the fibrous proteins. To illustrate this, load the structure of collagen, 1cgd.pdb, eliminate the solvent, and visualize the model in line drawing and by coloring the chains:
restrict protein;
trace only;
trace 100;
color chainRotate the structure and notice the interlacing of 3 strands. Check if the secondary structure matches your observation by show info. Note that there are no turns or bends.
Show the amino acid residues by show groups. Note that the molecule is composed only of Gly, Ala, Pro, and Hyp (hydroxyproline). This interlacing comprises the 3/10 helices of collagen. Provide the primary sequence by show sequence and note how these residues are distributed.
Also note how its stretch is greater than that of alpha helices, restricting the observation to the C chain only: restrict :C. In the 3/10 helix of collagen, the pitch is 0.94 nm (larger, therefore, than for \(\alpha\)-helix, 0.54 nm). To check this, simply double-click with the right mouse button on a part of the helix, and drag it to another part, until it covers approximately 0.9 nm.
Finally, see how the H-bonds are distributed in the structure:
Finally, see how the H-bonds are distributed in the structure:
calculate hbonds;
hbonds 50;
color hbonds yellow;
hbonds 0.5Now load another fibrous protein, fibroin from the silkworm, 1slk.pdb. First, observe the structure without the didactic visualization by cartoon or similar. At first glance, do they appear to have alpha helices? Check with show info. Note that there are 15 polypeptide chains in the molecule. To distinguish them, color chain. How do you expect the interaction between the chains to be?
calculate hbonds;
set hbonds backbone;
hbonds 50;
color hbonds whiteWhat is the amino acid composition (show groups)? Note that the structure is composed of a homopolymer of Ala and Gly, in addition to an acetylated N-terminus (ACE) and a methylated C-terminus (NME) in each chain. Now restrict the view to just four chains. For better visualization, select a white background: (and since the H-bonds are also white: ). Now: . Rotate the structure and observe its parallelism. What secondary structure is this? Type: rockets only. Observe the antiparallel orientation of the represented \(\beta\)-sheet section.
Now load the main chain of feline pyruvate kinase, 1pkm.pdb. Visualize it as usual, rotate the molecule and find out how many domains it has. Note that each domain constitutes a distinct compact unit. To make things easier:
select 116-219;color blue;
select 1-115;color green;
select 220-388;color red;
select 389-530;color pinkSometimes domains can form very similar structures, although in very different proteins. To observe this, load the microbial lactate dehydrogenase 1ldn.pdb. If you get the structure information (show info), you will see that the model consists of two crystallographic molecules. Add to the frame (frame) the microbial succinate dehydrogenase 1emd.pdb. For this additional loading, it is necessary that the structure is already in the root directory of Jmol. To do this, load the structure normally and save it by right-clicking and selecting File, Save. To add the structure to the previous molecule:
load append "1emd.pdb" # command to add models to the program screenPlace both molecules in the same frame, visualize them in strips (cartoon), but with different colors, and limit the pyruvate kinase to its A chain, enlarging the final image:
frame*
select all; cartoon only; select 1.1; color white; select 2.1; color green
select 1.1; restrict :A
zoom 0Finally, align the domain structures and rotate the molecules to visualize their similarity:
compare {2.1} {1.1} rotate translate 2Note that, although enzymes of microbial origin act on different substrates, the chains have structurally similar domains
Quaternary Structure
This additional level of organization (structural hierarchy) has already been discussed in the previous sections. The quaternary structure comprises proteins with more than one polypeptide chain (collagen, hemoglobin, IgG, for example). There is also the quinquenary structure, which corresponds to supramolecular associations formed by the combination of polypeptide chains with each other (protein complexes), or with nucleic chains (nucleoproteins), or lipid chains (biomembranes).
They are dimers, trimers, and oligomers, in general, each of which can perform similar or very distinct functions among its monomers. Functionally, quaternary proteins sometimes have complex interconnected actions, several active sites exhibiting sequential kinetics, as well as interaction sites with natural ligands to modulate their biological activity.
They are dimers, trimers, and oligomers, in general, each of which can perform similar or very distinct functions among its monomers. Functionally, quaternary proteins sometimes have complex interconnected actions, several active sites exhibiting sequential kinetics, as well as interaction sites with natural ligands to modulate their biological activity.
Hemoglobin
Among the most described quaternary structures is hemoglobin, one of several oxygen transport proteins, such as leghemoglobins (legumes), chlorocruorins (annelids), hemerythrin and hemocyanin (invertebrates). Human hemoglobin can be loaded by the file 1thb.pdb. Visualize it as a cartoon or trace, and color by structure (color structure).
What is the predominant structure? Are there any folds? How many chains does it have? Check with show info.
Hemoglobin exists in two distinct conformations}, T (low affinity for O\(_{2}\)) and R (high affinity for O\(_{2}\)). The equilibrium between these states results in the cooperativity of its binding with the four O\(_{2}\) molecules. In this PDB file, hemoglobin (Hb) is bound to O\(_{2}\) in only two chains, but crystallized in the T conformation.
Unlike myoglobin, which saturates with a single \(O_{2}\) molecule with a single affinity (hyperbolic saturation curve), hemoglobin binds to O\(_{2}\) with initially increasing affinities, producing a sigmoidal saturation curve. For example, the affinity of the 4th oxygen molecule is about 100 times greater than that of the 1st for hemoglobin.
This cooperativity translates into a conformational change produced in hemoglobin upon binding to O\(_{2}\), from its T state to the R state. Briefly, the motion of the heme plane is transmitted to the F helix by a His (helix F8, proximal histidine His87) bound to the Fe atom. Conformational changes in a unit are transmitted across the interfaces of the \(\alpha\)\(_{1}\)-\(\beta\)\(_{2}\) and \(\alpha\)\(_{2}\)-\(\beta\)\(_{1}\) subunits.
This difference between the affinities of Hb and Mb for O\(_{2}\) causes Mb to saturate at a pressure of 2.8 torr (venous capillaries, 30 torr), while Hb saturates at 30 torr (one hundred times higher; pulmonary alveoli - 100 torr).
This cooperativity translates into a conformational change produced in hemoglobin upon binding to O\(_{2}\), from its T state to the R state. Briefly, the motion of the heme plane is transmitted to the F helix by a His (helix F8, proximal histidine His87) bound to the Fe atom. Conformational changes in a unit are transmitted across the interfaces of the \(\alpha\)\(_{1}\)-\(\beta\)\(_{2}\) and \(\alpha\)\(_{2}\)-\(\beta\)\(_{1}\) subunits.
This difference between the affinities of Hb and Mb for O\(_{2}\) causes Mb to saturate at a pressure of 2.8 torr (venous capillaries, 30 torr), while Hb saturates at 30 torr (one hundred times higher; pulmonary alveoli - 100 torr).
For direct observation of Hb, visualize the model with coloring by cartoon chains, identify and highlight the heme prosthetic group (porphyrin ring):
select protein;
hide solvent;
cartoon only;
color chain;
show groups;
select hem
wireframe 100;color cpk
spin 10
delay 5
spin offIdentify the chains by clicking on each one. Also identify any possible ligands by typing show groups. Inositol hexaphosphate (IHP) can then be visualized by:
select ihp;wireframe 50;color cpkIHP is analogous to 2,3-BPG (bisphosphoglycerate) of non-mammalian organisms. Rotate the Hb and notice that the IHP is interacting with the chains in a cleft, near the B and D subunits of the protein.
2,3-BPG binds to the T state of Hb but not to the R state, thus reducing the protein’s affinity for oxygen. This allows about 40% free oxygen in venous blood. Fetal hemoglobin does not bind as strongly to 2,3-BPG, allowing a high affinity of O\(_{2}\) for the protein.
How do the Hb chains interact with each other? Which subunits bind to the IHP?
select protein; spacefill
label \%c # label the "c" chain of HbThe A and B chains represent an alpha/beta dimer. Note the extensive contacts between these chains, as well as between the C and D chains (also alpha/beta). But notice that there are very few contacts between the A and C chains, as well as between B and D, these pairs formed by alpha chains or beta chains. To visualize how the IHP with its six negative phosphate groups interacts with the protein:
select positive;color blueNow visualize only the C chain, colored from the N-terminal to the C-terminal region, with its heme group, and without the overlapping spheres:
select all; spacefill off; cartoon only;
restrict :c and not ihp;
color group;
select hem and not iron and :c;
wireframe 100;color cpk; zoom 0;
select iron and :c; spacefill 200;color cpkHow does molecular oxygen interact with hemoglobin?
“Turn off” the ribbon representation (): .
select protein and :c;trace only;trace 10; color groups # chain "b" with highlighted heme group
select (his58,his87,val62,phe43) and :c # selection of residues close to the heme group
define Obind selected # defines the selected residues with a label
select Obind; wireframe 50;color cpk # didactically represents the group
select oxy and :c;spacefill 150;color cpk # shows O2 in the structureNote the proximity of the side chains of His, Val and Phe to the center of the heme group. It can be better visualized with:
select (Obind, oxy and :c); dots on ("dots off" to omit the VDW clouds)To make it easier, name the selected residues at the alpha carbon:
select Obind :*.ca; label "\%n \%R"; color label whiteThe interaction of the ferric iron atom (Fe\(^{2+}\)) of the heme group occurs through six ligands, four of which are the tetrapyrrolic nitrogens of the prosthetic group of Hb, one of which is the nitrogen of the imidazole ring of the proximal histidine His87 and the sixth ligand is the molecular oxygen between the Fe atom and the side chain of the distal histidine His58. Rotate the structure and see why His87 is proximal. In addition, Val62 and Phe43 contribute to the hydrophobic environment of interaction with molecular oxygen. In the deoxygenated state the Fe atom of the heme group is only pentacoordinated.
Finally, a curiosity: the binding of oxygen displaces the porphyrinic Fe within the tetrapyrrole plane by only 0.4 angstroms, enough to displace the alpha helix in which proximal His87 is inserted closer to the heme.
Other quaternary proteins
There are a large number of quaternary proteins, some with dozens of polypeptide chains and/or with a large number of domains. During future discussions on metabolic activity, some of these proteins will be studied in greater depth, but for now, we will only visualize the structural complexity in a few examples.
Load an antibody, immunoglobulin G, 1igt.pdb. Rotate the molecule without changing its view, and you will see that it is a complex protein, in the classic shape of the letter “Y”, with at least three large domains linked by a few residues.
Also note that in the Console header, there are several sugars linked to the protein, configuring a glycoprotein. Then render the structure as usual: (cartoon only;color structure). Nominally, its chains are divided into heavy and light, the latter formed by \(\beta\) sheets that make contact with the antigen.
Now, which chains contact the cell surface? Rotating the structure makes it unclear. However, these domains of the heavy chains are linked to carbohydrates. Therefore, visualize the “trunk of the Y” by:
select hetero and not solvent;wireframe 50;color cpkAnother very complex quaternary structure is the photosystem of Rhodopseudomonas, 1prc.pdb. Load it and represent it by ribbons and coloring chains: cartoon only;color chain.
This photosystem is formed by two identical subunits (light and dark green) and two others (pink and red) linked to various photosynthetic pigments:
select hetero;wireframe 100;color cpkFor a final example of quaternary structure, the complexity of a bacterial chaperone called GroEl, a protein that helps other proteins fold correctly 1aon.pdb. Load the structure, provide an appropriate visualization with chain coloring, as before, and only then rotate the molecule to visualize its structural complexity. Proteins under folding interact in the central cavity of GroEl. Chaperones depend on ATP for their action, which can be observed by their identification with show groups:
select all; color grey; select adp;wireframe 300;color cpkFive-year structure
An example of the highest level of protein structural complexity, the quinquenary structure can be observed in nucleosomes (nucleoproteins), as in 1aoi.pdb. Load the molecule, and visualize it as ribbons and stained by structure.
Ribosomes also exhibit a 5-year structure, due to their interaction with nucleic acids. To do so, load the file 1qrs.pdb, and visualize the structure as ribbons and stained by structure or chain.