Morph Conformations

GTP-binding switch
(1tagA, 1tndA, morph intermediate)

Morph Conformations creates a trajectory that morphs between two or more structures. MD Movie is called to show the trajectory and can record it as a movie. Morph Conformations is under development (see limitations). A few example systems are listed below.

There are several ways to start Morph Conformations, a tool in the Structure Comparison category.

The different structures should be opened as separate models or submodels in Chimera and superimposed. The structures can have different numbers of residues or different sequences (homologs or mutants can be compared), but currently they must contain equal numbers of chains.

The next step is to populate the Conformations list with structures; the order in the list corresponds to the order in which they will be visited in the output trajectory. Clicking Add... brings up a dialog that lists the open molecule models. Clicking a model's name and then the Add button (or double-clicking the model's name) puts it in the Conformations list. The same model can be added more than once to produce a morph trajectory that visits the same conformation more than once. After the desired conformations have been added, the model-choosing dialog can be dismissed by clicking Close.

Clicking a line in the Conformations list designates that entry as the target of subsequent button actions:

Remove - remove the conformation
Up - move the conformation higher in the list (earlier in the trajectory)
Down - move the conformation lower in the list (later in the trajectory)

Each sequential pair of structures in the Conformations list will serve as the starting and ending points of one segment of a morph trajectory. A morph trajectory can have multiple segments. Within each segment, intermediates are generated by interpolating the positions of the atoms in common. Interpolation includes:

rigid-body transformations of atom groups partitioned by hinge regions. Hinges are identified as described in Krebs and Gerstein, Nucleic Acids Res 28:1665 (2000).
coordinate changes within the atom groups

How interpolated coordinates are generated, and in how many steps, can be specified independently for each segment. The following four settings apply to the segment preceding the structure currently highlighted in the Conformations list.

Interpolation method - how the rigid-body transformations will be calculated
- corkscrew (default) - Each group's starting and ending positions are related by a rotation about a center chosen to describe as much of the movement as possible, and a translation along the axis of rotation. These two components are interpolated.
- independent - Each group's starting and ending positions are related by a rotation about the group's center of mass, and a translation. These two components are interpolated.
- linear - Each group's starting and ending positions are related by a translation, which is interpolated.
Interpolation rate - how conformational changes will be distributed across the segment
- linear (default) - coordinate changes will be distributed approximately evenly
- ramp down - coordinates will change most rapidly near the starting conformation
- ramp up - coordinates will change most rapidly near the ending conformation
- sinusoidal - coordinates will change most rapidly halfway between the starting and ending conformations
Interpolation steps [K] - the starting and ending conformations of the segment will be K steps apart (default 20); K–1 intermediates will be generated
Force Cartesian intermediates (off by default) - whether within-group coordinate changes should be interpolated strictly in Cartesian space. Otherwise, internal coordinates will be used for the interpolation where possible. Using internal coordinates is slower but produces less distortion. A trajectory made with Cartesian forcing may be acceptable if few atomic details will be shown (for example, if only ribbons will be displayed).

The Minimize setting applies collectively to all segments of the morph trajectory:

Minimization steps [N] - N steps of minimization (default 60) will be applied to each intermediate
Minimization requires the correction of structural inconsistencies, addition of hydrogens, and association of atoms with force field parameters. Dock Prep, AddH, Add Charge, and Minimize Structure are called in no-GUI mode to perform these tasks; that is, the dialogs will not appear, but each tool will execute with default settings. When minimization is turned on, interpolation to generate an intermediate will use the minimized coordinates of the prior intermediate.

Clicking Create hides the dialog (unless the option to Keep dialog up after Create is checked) and initiates the calculation. The MD Movie tool will be called to display the morph trajectory, and any specified Action on Create will be performed:

none
show Model Panel - open the Model Panel (allowing the input structures to be hidden or closed)
hide Conformations - hide the input structures

The trajectory will be opened as a separate model. Coordinates for the atoms in common from the segment endpoints (input structures) and the intermediates comprise the frames of the trajectory. The MD Movie tool can be used to record the trajectory as a movie file. If the movie includes ribbons, consider re-evaluating secondary structure at each frame as described below. After the trajectory has been viewed, it can be saved as a PDB file.

Hide hides the Morph Conformations dialog, Quit exits from the tool, and Help opens this manual page in a browser window. If the Morph Conformations dialog has been hidden or becomes obscured by other windows, it can be resurrected with the Raise option for its instance in the Tools menu. Multiple copies of the Morph Conformations dialog can coexist, possibly with different settings and/or listed conformations.

Superimposing Structures

The apparent motion across a morph trajectory depends on how the input structures are superimposed; matched regions will remain approximately steady.

There are several ways to superimpose structures in Chimera:

MatchMaker (command equivalent matchmaker) superimposes structures by constructing a sequence alignment and then performing a least-squares fit of the aligned residue pairs, using one atom per residue
the match command allows detailed specification of which atoms to fit
structures can be manipulated interactively and toggled between active and immovable states

The first two methods allow iterative exclusion of poorly superimposed atoms from the fit.

Atoms in Common

Intermediates are generated by interpolating between starting and ending structures. Interpolation requires a pairing of atoms in the starting structure with atoms in the ending structure. Only atoms common to both segment endpoints are included in the morph trajectory.

Residues are paired by aligning the sequences of their chains. The sequence alignment is performed using the matchmaker defaults (Needleman-Wunsch algorithm, BLOSUM-62 matrix, secondary structure reassignment with ksdssp, 30% secondary structure scoring, etc.), except that the Nucleic matrix is used for nucleic acids. Only the sequence alignment stage of matchmaker is performed, not the superposition of structures. Morph Conformations does not change how the input structures are superimposed.

Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue. For example (disregarding hydrogens), phenylalanine and tyrosine have in common all atoms of phenylalanine.

Example Systems for Morphing

A few example systems are listed here, including chain IDs. Currently it is necessary to delete other peptide chains before morphing between the structures.

Different conformations of the same or nearly the same protein:

alpha-transducin GTP-binding switch (see the figure): 1tagA (complex with GDP), 1tndA (complex with GTP analog)
thioredoxin reductase ball-and-socket movement: 1tdeA (complex with FAD), 1f6mA (complex with FAD and NADP+ analog)
dehydrosqualene synthase (see the Structure Analysis and Comparison tutorial): 2zcoA (uncomplexed), 2zcpA (complex with substrate analogs)

Different but homologous proteins:

phosphomannomutases, pairwise sequence identity ~50-70%: 2i55C (Leishmania PMM complex with glucose bisphosphate), 2fucA (human PMM1), 2amyA (human PMM2)
pectate lyases from different organisms, sequence identity ~35%: 1jtaA, 1bn8A

As structures become less similar in sequence, a morph trajectory between them is more likely to contain backbone "breaks," corresponding to gaps in the sequence alignment that defines the atoms in common.

Limitations

MD Movie does not automatically re-evaluate secondary structure. MD Movie does not automatically recompute secondary structure assignments as coordinates change across a trajectory. This is relevant when ribbons are displayed and the conformational changes are large enough to alter secondary structure assignments. To recompute secondary structure at each frame, use a per-frame script in MD Movie that includes the Chimera command ksdssp.

Structures with different numbers of chains are not handled. Currently, a morph trajectory can only be generated from input structures with equal numbers of biopolymer chains. Extra chains in the input models should be deleted beforehand or split into separate models not used in morphing.

Sequences should be easy to align. The sequences of the structures must be aligned to determine the atoms in common for interpolation. When the sequences are dissimilar, parts of the sequence alignment may be wrong, leading to a jumbled and unattractive morph trajectory. A possible future improvement is to allow users to specify residue pairings with an input sequence alignment.

Minimization limitations. The Minimize Structure tool has its own set of limitations.

UCSF Computer Graphics Laboratory / May 2008