Any questions on the material from the previous lecture?
Section 4.4: The α Helix
The α helix is the most common secondary structural motif found in proteins
It was the first significant biomolecular structural building block to become known
Predicted by Linus Pauling in 1951, it was subsequently confirmed 6 years later by experimental data
Pauling developed his prediction while sick in bed, playing with some pieces of paper
Prior to that time, the structural nature of proteins was shrouded in mystery
Pauling's great insight helped to open up the era of structural molecular biology (along with Watson and Crick's model of DNA)
Geometry of the α Helix
Molecular features are commonly measured in units of Angstroms (Å), with 1 Å = 1 x 10-10 meters
(although the text uses nanometers, nm)
The α helix has a general cylindrical shape, and can vary in length from 5 to 50 Å or more
The vast majority of alpha helices are right-handed (clockwise rotation combined with forward translation)
The specific geometry of the helix is characterized by its
Rotation / residue = 100 ° (rotation around the helix axis from one residue to the next)
Rise = 1.5 A (translation along axis from one residue to the next)
These 'per-residue' parameters can be converted to 'per-turn' parameters:
Residues / turn = 3.6 (number of residues in one full rotation of 360 °)
Pitch = 5.4 A (translation along axis for one full rotation of 360 °)
Geometry of the α Helix
The α Helix is Stabilized by Hydrogen Bonds
The α helix results from hydrogen bonding between main-chain CO and NH groups
Hydrogen bonds form between the carbonyl of a residue and the amino of another residue four along in the
sequence:
α-Helix in PDB Model 1A6M
load 1A23.pdb (oxidoreductase)
show backbone
highlight helix
center on helix
hide rest of mol
calc hbonds
show helix residues
φ and ψ angles of the α Helix
The φ and ψ angles of residues that form the α helix have characteristic values
As shown in the Ramachandran diagram, right-handed α helices have (φ, ψ) values
in a region centered around (-70°, -50°):
The Helix is a Common Organizational Feature
The α helix is a specific kind of helix that forms in proteins, but other kinds of
helices also occur in biomolecules
There are single chain helices that are similar to the α helix, such as the 310
helix and the π helix
There are also 'super' helices, which are formed from two or more α helices wrapped together (coiled coils)
An example is keratin, a structural protein found in hair:
Section 4.5: β Sheets
The β sheet was the second protein structural motif to be predicted, also by Pauling (with Corey)
It also turned out to be the second most significant type of protein secondary structure
The β sheet is composed of two or more individual strands that form hydrogen bonds with each other
β sheets are more structurally diverse than α helices
They are mostly flat, but can have a variety of twists and bends in their shape
The individual strands can also be aligned in two different orientations: parallel and anti-parallel
Geometry of Anti-Parallel &beta Sheets
In an antiparallel β sheet, the CO and NH groups of a residue on one strand form hydrogen bonds
with the corresponding NH and CO groups of a residue in an adjacent strand running in the opposite direction:
Geometry of Parallel &beta Sheets
In a parallel β sheet, the NH group of a residue hydrogen bonds to the CO group of an adjacent strand
residue, while the CO group hydrogen bonds to the NH group of a different residue two positions farther along on the
adjacent strand:
More β sheet geometry
In the strands of both parallel and antiparallel β sheets, the main chain is nearly fully extended,
with side chains alternately projecting above and below the sheet:
The spacing between successive residues is greater than in the α-helix, and is around 3.5 A on average
β-Sheet in PDB Model 1A6M
load 1BJI.pdb (neuraminidase)
show backbone
highlight sheet
center on sheet
hide rest of mol
calc hbonds
show sheet residues
More β sheet geometry
In addition to being purely parallel or antiparallel, β sheets can be mixed, with strands
running in both parallel and antiparallel directions:
φ and ψ angles of the β Sheet
Like the α helix, the φ and ψ angles of residues in β strands have characteristic values,
but with a greater degree of variance
As shown in the Ramachandran diagram, β strand residues have (φ, ψ) values
in an extended region centered around approximately (-100°, 140° ):
β-Barrels
β sheets can fold around to form closed cylindrical structures such as β-barrels:
3D Molecular Visualization
A better appreciation of protein structure can be gained by viewing models in 3D space
There are a number of software programs for doing this (see software section on course web page)
We'll look at two of them today, RasMol and Jmol
In order to view a protein structure, you need to get a model of it. Models can be downloaded from the Protein Data Bank.
This requires knowing a PDB code for a model (4 digit ID such as '1FFK')
Currently, there are only 3D models for a very small subset of biomolecules, but even so,
there are more than 38,000 models in the PDB to investigate!
Getting Models from the Protein Databank
A starting point for finding a model of interest is to do a search on PubMed (see link on course web pages)
Example: to find a model of the structure of insulin shown at beginning of Ch. 3:
In PubMed, enter keywords "insulin" "crystal structure" "PDB"
Look up reference 'Wan et al, 2005, Biochemistry'
Access the article through the UM lib electronic journals
Download pdf or view html full text of article
Read entire article very carefully OR just search for 'deposited', 'PDB' or 'Protein Data Bank' in article
Found PDB code 1XW7 (also find codes of related or earlier models such as 4INS, 1ZEG)
Go to the PDB, enter the code and download the model (if too slow, try the Beta PDB site)
Download PDB format, uncompressed
Viewing a Model in RasMol
RasMol was one of the first open source molecular viewers for personal computers, created by Roger Sayle
back in the 1990's. It's no longer actively developed, and showing its age, but it is small, simple and fast.
It has also defined somewhat of a 'standard' command set for molecular viewing that has been subsequently
supported by newer viewers such as Jmol
The recent distribution consists of just a single executable file ('raswin.exe') and two help files,
'raswin.hlp' and 'rasmol.txt'. Run the executable file by double-clicking on it from Windows Explorer
or by entering its full path in the 'Run' box in the Start menu
To load and view a model in the program, do the following:
Choose 'File', 'Open' from the main menu, then navigate to the directory containing the downloaded PDB file,
then select the file and click 'Open' (can also drag and drop)
Use the mouse to rotate (LBUTTON), translate (RBUTTON) and zoom (SHIFT + LBUTTON)
Switch to the 'Command Line' window to enter commands
Select all or part of the model and then turn on various display representations
Refer to the user manual for more information on command line syntax
Viewing a Model in Jmol
Jmol is a newer program than RasMol, with better graphics and is being actively developed. It is
also cross-platform, open source, free software, available at .http://jmol.sourceforge.net.
It requires Java version 1.4 or greater to be installed
To run the standalone version, from Windows, double-click 'jmol.bat' or enter the full path to it in
the Start menu 'Run' box
To load and view a model in the program, do the following:
Open a PDB file, or drag-and-drop, as with RasMol
Use the mouse to rotate (LBUTTON), translate (DOUBLE-CLICK + LBUTTON) or zoom (SHIFT + LBUTTON) the view
Select 'File', 'Script...' from the menu to open the RasMol 'Command Line' window (most RasMol commands are supported)
Refer to the user manual for more information on command line syntax (RasMol docs are better)
Viewing the Model of Insulin: PDB 1XW7
The following commands show how to adjust the graphical display so that the disulfide linkages in insulin
are highlighted:
Open the PDB file, then open the 'RasMol Scripts' window
Type 'select all' to select everything
Type 'spacefill off; wireframe off' to turn off the default 'ball and stick' display
Type 'select :A or :B' to select the first two chains
Type 'wireframe 1' to draw all bonds as very thin lines
Type 'color grey' to de-emphasize most of the structure
Type 'center (:A or :B)' to center rotation around the A and B chains
Type 'backbone 100' to show the backbone
Click on a backbone element and observe the residue info reported in the Command window
Type 'select *:A.SG or *:B.SG' to select all the sulfur atoms in the A and B chains
Type 'color cpk' to restore their default coloring
Type 'wireframe 100' to prominently show the 3 disulfide bonds
