Interactive protein manipulation Page: 4 of 8
This article is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided to UNT Digital Library by the UNT Libraries Government Documents Department.
Extracted Text
The following text was automatically extracted from the image on this page using optical character recognition software:
coil region's behaviour during interaction. This feature can also be
used to "touch up" already optimized protein structures by resetting
partially unraveled structures to their default shapes.
4.3 )-strand Adjustment
fl-strands have a certain amount of flexibility to adjust to their envi-
ronment in sheets. Coherent shape changes result from changing all
0 angles by the same increment, or all u angles by the same incre-
ment. Richardson and Richardson [10] suggest a different basis for
this two-dimensional space of coherent shape changes, which has a
more comprehensible geometric meaning. Twist increments both 0
and u by the same amount, while pleat increments all 0 angles by
the same amount, and decrements all u angles by this amount.
Since the dihedral angles of a fl-strand are close to 1800, the
backbone forms a zig-zag pattern, with the residues on alternating
sides. Thus changes in 0 and u of period two also have coherent
effects on the strand shape. Curl, a period two change also sug-
gested in [10], decreases the 0 and increases the u of odd num-
bered residues, counting from the beginning of the strand, and
does the opposite for even numbered residues. To fill out the four-
dimensional space of period two changes to 0 and u, we added a
fourth basis element, not described in [10], which we called braid.
It increases both 0 and u for odd numbered residues, and decreases
them for even numbered residues.
These changes were implemented in the form of four dials,
which can coherently change the shape of a selected fl-strand in
the interactive user interface. These dials are useful in adjusting a
strand's shape in order to form more hydrogen bonds with adjacent
strands in a fl-sheet.
4.4 Structure Manipulation
Our program uses inverse kinematics (IK) to transform pieces of a
protein with respect to each other, without breaking chemical bonds
in the protein backbone between those pieces [8]. As mentioned in
Section 1.1, coil regions are flexible because they do not pose tight
constraints on their residues' dihedral angles. Thus, they can serve
as "buffers" for transformations of protein parts.
To begin manipulation, a user selects a single secondary struc-
ture, typically an a-helix or a fl-strand. The program then renders
the "3D interaction widget," a translucent green box surrounding
the selected structure, see Figures 7 and 8. The widget can be trans-
lated or rotated by dragging it with the mouse. Additionally, a user
activates one or more coil regions that will serve as buffers for sub-
sequent manipulation. In Figures 7 and 8, active coil regions are
highlighted in yellow.-'4 W
Figure 7: A fl-strand has been selected and is surrounded by the 3D
interaction widget. The two coil regions surrounding the central a-
helix have been activated for manipulation. Left: before dragging
the widget; right: after dragging the widget.
In the simpler case, all active coil regions are on the same side of
the selected structure (either before it or after it according to chain
order). When, for example, all coil regions are before the selectedstructure, then dragging the interaction widget will transform the
selected structure, and the rest of the protein after it, with respect to
the part of the protein before the first active coil region. All active
coil regions will change shape, and all structures between active
coil regions will undergo rigid body transformations, as dictated by
the IK algorithm. This mode of interaction allows a user to align
protein parts to each other, especially to form fl-sheets by manually
aligning fl-strands.
In the more complex case, where active coil regions exist on both
sides of the selected structure, dragging the widget will move the
selected structure with respect to the two parts of the protein before
and after any active coil regions. Those two parts, even though un-
related according to chain order, will not move with respect to each
other. As in the simpler case, shape changes of active coil regions
and transformations of intermediate structures are guided by the IK
algorithm. This second interaction mode can be used to fine-tune
the placement of intermediate parts in an already assembled struc-
ture, see Figure 8.
Figure 8: An a-helix has been selected and is surrounded by the
3D interaction widget. Both surrounding coil regions are activated
for manipulation. Left: before dragging the widget; right: after
dragging the widget.
4.5 Inverse Kinematics
Every rotatable single covalent bond along a protein's backbone can
be interpreted, in an IK sense, as a joint with a single axis of uncon-
strained rotation. After a user selects a structure and activates coil
regions, and before manipulation begins, the program constructs a
linked assembly by creating two rotational joints for each amino
acid residue2 inside each active coil region. Let us assume that
all active coil regions are before the selected structure according to
chain order3. In this simpler manipulation case, the linked assembly
is rooted at the rear end of the last structure before the first active
coil region, and the "leaf" joint is connected to the front end of the
selected structure, see Figure 9.
Creating a linked assembly in the described way results in intu-
itive behaviour during manipulation. The selected structure, and the
rest of the manipulated protein behind it, are treated as a rigid body
and move together following the motion of the interaction widget.
If the interaction widget is moved into a position/orientation that
cannot be realized by setting dihedral angles for the currently ac-
tive coil regions, the IK algorithm will automatically approximate
the requested position/orientation in a least-squares sense.
A more complex manipulation case occurs when active coil re-
gions are located on both sides of the selected structure. The current
version of our manipulation code handles this case by creating two
independent linked assemblies: one for all active coil regions be-
fore the selected structure, and one for all active coil regions after
2In the case of proline, the IK algorithm only creates a single joint since
proline has a rigid N-C bond.
3The case where all active coil regions are behind the selected structure
is symmetrical.
Upcoming Pages
Here’s what’s next.
Search Inside
This article can be searched. Note: Results may vary based on the legibility of text within the document.
Tools / Downloads
Get a copy of this page or view the extracted text.
Citing and Sharing
Basic information for referencing this web page. We also provide extended guidance on usage rights, references, copying or embedding.
Reference the current page of this Article.
SNCrivelli@lbl.gov. Interactive protein manipulation, article, July 1, 2003; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc875770/m1/4/: accessed April 23, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.