MovieMaker: a web server for rapid rendering of protein motions and interactions.

Abstract

MovieMaker is a web server that allows short ( approximately 10 s), downloadable movies of protein motions to be generated. It accepts PDB files or PDB accession numbers as input and automatically calculates, renders and merges the necessary image files to create colourful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating (i) simple rotation, (ii) morphing between two end-state conformers, (iii) short-scale, picosecond vibrations, (iv) ligand docking, (v) protein oligomerization, (vi) mid-scale nanosecond (ensemble) motions and (vii) protein folding/unfolding. MovieMaker does not perform molecular dynamics calculations. Instead it is an animation tool that uses a sophisticated superpositioning algorithm in conjunction with Cartesian coordinate interpolation to rapidly and automatically calculate the intermediate structures needed for many of its animations. Users have extensive control over the rendering style, structure colour, animation quality, background and other image features. MovieMaker is intended to be a general-purpose server that allows both experts and non-experts to easily generate useful, informative protein animations for educational and illustrative purposes. MovieMaker is accessible at http://wishart.biology.ualberta.ca/moviemaker.

Full text

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MovieMaker: a web server for rapid rendering of
protein motions and interactions
Rajarshi Maiti1,2, Gary H. Van Domselaar1,2and David S. Wishart1,2,*
1Department of Computing Science and2Department of Biological Sciences, University of Alberta,
Edmonton, AB, Canada T6G 2E8
Received February 13, 2005; Revised and Accepted April 20, 2005
ABSTRACT
MovieMaker is a web server that allows short (?10 s),
downloadable movies of protein motions to be gen-
erated. It accepts PDB files or PDB accession num-
bers as input and automatically calculates, renders
and merges the necessary image files to create col-
ourful animations covering a wide range of protein
motions and other dynamic processes. Users have
the option of animating (i) simple rotation, (ii) morph-
ing between two end-state conformers, (iii) short-
scale, picosecond vibrations, (iv) ligand docking,
(v) protein oligomerization, (vi) mid-scale nano-
second (ensemble) motions and (vii) protein folding/
unfolding. MovieMaker does not perform molecular
dynamics calculations. Instead it is an animation
tool that uses a sophisticated superpositioning
algorithm in conjunction with Cartesian coordinate
interpolation to rapidly and automatically calculate
the intermediate structures needed for many of its
animations. Users have extensive control over the
rendering style, structure colour, animation quality,
background and other image features. MovieMaker is
intended to be a general-purpose server that allows
both experts and non-experts to easily generate
useful,informativeproteinanimationsforeducational
andillustrativepurposes.MovieMakerisaccessibleat
http://wishart.biology.ualberta.ca/moviemaker.
INTRODUCTION
Protein structures are not static. Indeed, proteins vibrate,
twist, bend, open, close, assemble and disassemble in a variety
of ways over many different time scales. Protein motions
and conformational accommodation actually lie at the heart
of many important protein–ligand interactions, including
protein–DNA binding (1), enzyme–substrate interactions (2),
muscle contraction (3) and oligomerization (4). Owing largely
tothecontinuingdevelopmentsofX-raycrystallography,NMR
spectroscopy and computational molecular dynamics (MD),
the temporal and spatial scales involved in protein motions are
now becoming better understood (5). Small-scale (<1.0 s)
motions over short periods of time (picoseconds) can be mod-
elled or measured using either X-ray thermal B factors (6),
NMR order parameters (7) or shorter (<1 ns) MD simulations.
Mid-scale motions (1.0–4.0 s) tend to take place over longer
periods of time (hundreds of picoseconds to nanoseconds) and
can be discerned by comparing NMR structure ensembles,
lookingattheX-raystructuresofdifferentcrystalisomorphsor
running long (10–100 ns) MD simulations. Large-scale
motions (5–30 s), which may take microseconds to complete,
are typically evident only by comparing two different states
or experimentally determined structures of the same molecule
(say, bound and unbound). These motions cannot normally be
modelled via MD.
The fact that molecular motions play such an important
role in protein function underlies the growing need to be
able to illustrate or visualize these motions in an informative
manner. Several commercial MD packages allow molecular
‘movies’ to be screen-captured and displayed via standard
computer presentations. However, relatively few biologists
are familiar with, nor do they have the expertise to use,
these relatively sophisticated and expensive software tools.
Likewise, not all motions (especially some of the more inter-
esting or larger-scale ones) can be captured using off-the-shelf
MD simulations.
More recently, Mark Gerstein at Yale University has deve-
loped an excellent and easy-to-use web server (the Morph
server) which allows non-expert users to animate and visualize
certain types of protein motions through the generation of
short movies (8). This tool specifically models larger-scale
motions or ‘morphs’ by interpolating the structural changes
between two different protein conformers and generating a set
of plausible intermediate structures. A hyperlink pointing to
the morph results is then emailed to the user. The primary
focus of the Morph server has been to facilitate research into,
analysis and classification of different kinds of large-scale
molecular motions of monomeric proteins. As such it is not
*To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart@ualberta.ca
? The Author 2005. Published by Oxford University Press. All rights reserved.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access
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areattributedastheoriginalplaceofpublicationwiththecorrectcitationdetailsgiven;ifanarticleissubsequentlyreproducedordisseminatednotinitsentiretybut
only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oupjournals.org
W358–W362
doi:10.1093/nar/gki485
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intended to be a general molecular animation tool capable of
simulating all aspects of macromolecular motion such as fold-
ing/unfolding, docking, oligomerization, multimeric protein
motions, vibrational motions and structural ensemble motions.
For instance, the Morph server offers only limited user control
over rendering, animation parameters, colour and point of
view. Likewise, the methods used to generate the movies
are computationally intensive and can require up to 1 h of
CPU time before completion. Furthermore, the Morph server
does not allow the modelling of motions from a single input
structure or from more than two input structures. This is some-
what limiting if one is interested in modelling motions from
NMR structure ensembles or if one has only a single X-ray
structure of a given protein. Additionally, the Morph server
does not support the visualization of other kinds of protein
motions, such as folding/unfolding, or of docking and self-
assembly events involving two or more structures.
Here we wish to describe a general molecular animation
server that allows a wide range of motions and dynamic events
to be animated and offers a much greater range of user control
over rendering and animation parameters. This server, called
MovieMaker, allows small-, medium- and large-scale motions
to be rendered using as few as 1 and as many as 50 input
structures. It allows users full control over the rendering style,
molecular colouring scheme, background, point of view, rota-
tion rate and animation quality. It also employs a simplified
Cartesian coordinate interpolation approach coupled with an
intelligent superposition algorithm that allows most kinds of
molecular movies to be rendered automatically in less than
1 min. Unlike any other animation tool that we are aware of,
MovieMaker also allows users the option of creating movies
of protein folding/unfolding as well as molecular docking or
self-assembly (oligomerization) of two or more molecules.
Rather than being a specialized analytical tool, the main pur-
pose of MovieMaker is to quickly and conveniently generate
realistic, downloadable animations of protein motions that
can be used by non-specialists for a variety of educational
or instructive purposes.
PROGRAM DESCRIPTION
MovieMaker supports seven kinds of animations: (i) simple
rotation, (ii) morphing between two end-state conformers,
(iii) small-scale vibrations, (iv) small molecule docking,
(v) self-assembly or oligomerization, (vi) mid-scale (structure
ensemble) motions and (vii) protein folding/unfolding. The
type of animation is dependent on both the input data and
the type of animation selected by the user from a pull-down
menu box. The MovieMaker home page presents the user with
the type of movie choices that one can generate (Figure 1)
along with an extensive gallery illustrating the types of
motions that can be modelled. Upon selecting the appropriate
movie type, the user is presented with input boxes for file
uploads and various display options. The input for all Movie-
Maker animations is one or more PDB-formatted files con-
taining one or more protein structures. These can be directly
uploaded to MovieMaker using the file selector boxes or alter-
natively one or more PDB accession numbers can be provided
and the program will automatically retrieve the appropriate
PDB files from the RCSB website (9).
The simplest motion to render in MovieMaker is a basic
rotation. The rotation animation is intended to allow all sides
of a given structure to be conveniently and continuously
viewed. Once the rotation option is selected, only a single
PDB file needs to be provided. If multiple structures are
found in a single PDB file, the program either treats the
ensemble as a single oligomeric structure or the user can select
a single chain from that file. To generate the rotation anima-
tion, MovieMaker takes the input file and applies a series of
standard x, y or z axis rotations to the structure(s). Users have
the option of changing the speed and extent of the rotation by
adjusting the number of frames in the animation (the default
is a rotation of 360? in 10? increments). Additionally, through
the viewing options section located below the data entry sec-
tion, users may change the orientation of the molecule (by
rotating along the x, y or z axes), the molecular rendering style
(backbone, CPK, ball-and-stick, ribbon), molecular content
(backbone only, all atoms, selected side-chains), image size
and molecular colour (by secondary structure, rainbow, by
chain, single uniform colour). All renderings are performed
using the molecule visualization program MOLSCRIPT (10).
Another freeware program called gifmerge (http://www.lcdf.
org/gifsicle/) is then used to string the output images from
MOLSCRIPT to create an animated GIF. This animated
GIF is looped continuously to provide a smooth visualization
of the rotation process. The animations are instantly viewable
on the user’s web browser and may be saved by right-clicking
on the animation image and selecting ‘save file’ or ‘save
image’. A typical movie file is ?500 kB. MovieMaker also
generates a downloadable set of PDB text files that users can
use to generate specific images or regenerate animations using
their own molecular rendering software.
Small molecule docking requires only a single PDB file
containing two or more molecular entities that are already
bound. Once the small molecule docking option is selected,
the MovieMaker program automatically parses the input file
and identifies all molecular entities (small molecules and
protein chains). Users must then select one protein entity and
one small molecule entity. To generate a pre-docking or two-
component state, MovieMaker then calculates the centre of
masses for the protein alone, the small molecule alone and the
complex together. A vector is then drawn from the complex’s
centre of mass to the small molecule’s centre of mass. This
vector defines the direction that the small molecule entity
must move in to create a pre-docking state. To generate a
pre-docking state, the small molecule is translated 15 s
along this vector and randomly rotated (between 15? and
60?) about its individual x, y and z axes. MovieMaker then
calculates a series of intermediate positions by incrementally
rotating and translating the small molecule until it reaches its
original bound position. The default increment is 1/20 of the
original translation/rotation. As with the rotation option, users
have full control over colouring, point of view and rendering
styles. Note that the small molecule can be rendered (CPK,
ball-and-stick) and coloured in a variety of ways.
Oligomerization and self-assembly are handled in a very
similar manner to small molecule docking. As with docking,
only a single PDB filecontaining two ormore macromolecules
is required. However, when the self-assembly option is selec-
ted all macromolecular entities within the PDB file will be
separated and reassembled. Users do not have the option to
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select a subset of molecules that are to be assembled or
docked. The same centre of mass calculations, direction vector
calculations, rotations and translations are repeated for all
subunits in the oligomer to create a preliminary disassembled
state. The complex is reassembled using the reverse rotation
and translation operations. Note that both the docking and
oligomerization animations are inherently ‘rigid’ dockings.
No internal motions are currently generated for the interacting
proteins or ligands.
When MovieMaker’s small-scale or vibrational motions
option is selected only a single PDB file (containing a single
chain) is needed. The key trick to most of MovieMaker’s
motion generation is to use Cartesian coordinate or torsion
angle interpolation between a ‘perturbed’ state and a ‘ground’
state conformation. In Cartesian interpolation the intermediate
positions between two states or positions are calculated in
a linear fashion based on the coordinates between the two
end-points and a chosen increment. The resulting images
therefore depict a pathway that two conformers can take
when morphing from one to the other. To create a perturbed
state, MovieMaker generates random displacements of the
x, y and z coordinates of between 0.0 and 1.0 s for all
heavy atoms in the original PDB file according to the mag-
nitude of their corresponding B factors. Specifically, the ad
hoc formula B = 100(|Dx| + |Dy| + |Dz|) is used to calculate
the x, y and z atomic displacements. If no B factors are present
in the file a default value of 60 is used. These perturbed
structures are then rendered and infinitely looped to create
the illusion of a long-term MD simulation.
When the structural ensemble motion option is selected,
users must provide a PDB file containing two or more copies
of the same protein molecule. This can include an NMR struc-
ture ensemble (typically 20–40 structures) or multiple copies
(2–10) of the same protein in a single unit cell from a standard
X-ray structure. If the molecules are not identical, Movie-
Maker will provide a warning and cancel the rendering opera-
tion. MovieMaker uses a recently developed superpositioning
tool called SuperPose (11) to intelligently and automatically
compare, rank and superimpose all structures in the ensemble
or unit cell. Moving from the most similar pair to the least
Figure 1. A screenshot of the MovieMaker home page showing the different animation options.
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similar remaining pair of superimposed structures in the
ensemble, Cartesian coordinate interpolation is performed
to generate a series of intermediate structures. MovieMaker
automatically takes into account the number of structures in
the ensemble to select an optimal number of intermediate
structures for a smooth, fluid transition between states. As
with most other animations in MovieMaker, the ensemble
motion option always morphs the structure from a starting
state to a perturbed state and back so that the movie can be
placed into a smoothly running infinite loop.
To depict large-scale motions MovieMaker requires two
PDB files, each containing the same protein but in a different
conformation. As with the ensemble motion option, Movie-
Maker employs the SuperPose program to intelligently super-
impose the two structures and identify any large-scale hinge
or domain motions. Displacements between the two states are
categorized (<2 s over >90% of the protein length or >2 s
over >10% of the protein length) by calculating a difference
distance matrix between the two superimposed coordinates.
After the displacement has been categorized, intermediate
structures are created by interpolating between the two end
conformers. Both small motions and larger hinge motions can
be mapped using the Cartesian interpolation method. Minor
distortions creep in for very-large-scale hinge motions, but
these distortions can be almost removed by increasing the
number of intermediate structures generated between the
two conformations.
When the protein folding/unfolding optionis selected only a
single PDB file (containing a single, folded protein chain) is
needed. For this kind of animation, coordinate interpolation
must be done in torsion angle space as the intermediate struc-
tures simply get too distorted during the unfolding process. In
torsion angle interpolation the native structure is regenerated
using phi/psi/omega angles derived from the PDB file. This
re-rendering in torsion space requires additional structural
optimization and can take several minutes, depending on
the size of the structure. Once rendered in torsion angle
space, the backbone phi/psi angles are iteratively ‘relaxed’
to an unfolded or extended set of phi/psi torsion angles of
?160? – 10?. All intermediate structures are rendered using
the same torsion angle structure generator (called PepMake).
As always,MovieMakermorphsthe structurefromthe starting
state (folded) to the end state (unfolded) and back so that the
movie can be placed into a smoothly running infinite loop.
RESULTS AND DISCUSSION
To assess the performance of MovieMaker we chose 30
random protein structures from the PDB consisting of single
monomers, complex heteromultimers, NMR ensembles and a
variety of proteins with bound ligands. The proteins or protein
complexes ranged in size from 56 residues to 1450 residues.
We assessed the performance of the program using three
criteria, (i) realism, (ii) accuracy and (iii) speed, on as many
different types of motions as possible. Assessing realism is
somewhat qualitative and highly visual. However, we wanted
tomakesure thatthe resultinganimationsweresmoothanddid
not lead to any obvious ‘breaches’ of the laws of physics such
as atoms or chains passing through one another or serious
distortions in secondary structure. Of nearly 30 animations
studied using the default parameters we found only 4
animations that exhibited a mildly unrealistic chain distortion
or a physically unrealistic event. These were confined prim-
arily to animations with very large hinge movements. Apart
from these ‘breaches’, vibrational and ensemble motions,
rotations, docking, folding and hinge motions all appeared
to be performed very well with no obvious problems.
In terms of assessing the accuracy or realism of the small-
scale vibrational and structural ensemble motions, we used
myoglobin(153residues,PDB1MYF)andthepointed domain
(110 residues, PDB 1BQV) to visually compare Movie-
Maker’s movies with those generated via the MD simulation
program GROMACS (www.gromacs.org). Comparing a
short (10 ps) MD simulation for myoglobin calculated by
GROMACS with the motion calculated by MovieMaker’s
small-scale vibrational motion generator, one can see very
little difference (the two movies are available on Movie-
Maker’s gallery page). Similarly, a long-term (2.5 ns) MD
simulation from GROMACS for the pointed domain appears
tobe qualitativelysimilartothe ensembleanimationgenerated
by MovieMaker (see the gallery page). Finally hinge motion
movements were tested with DNA polymerase beta, cyano-
varin N, recoverin and calmodulin proteins. The morphs
generated by MovieMaker and the Yale Molecular Motions
server appear to be essentially identical for these hinge motion
movements.
Table 1 lists the approximate CPU time (2.0 GHz processor
with 512 MB RAM) taken for each of the seven types of
motion supported by MovieMaker. Obviously these times
will vary with the load on the server and the speed of the
user’s Internet connection. It is clear that the rotation anima-
tion is the fastest (10 s), and the motion for the ensemble of
structures is the slowest (260 s). Most animations are gener-
ated in <30 s. This underlines one of the key strengths of
MovieMaker—its speed. Using conventional MD or non-
conventional MD simulations (such as adiabiatic dynamics,
activated dynamics or Brownian dynamics) would typically
take many hours or days of CPU time.
CONCLUSION
It is important to emphasize that MovieMaker is a molecular
animation server, not a modelling or MD server. In animation
or simulation one attempts to mimic reality using a variety
of ad hoc rules that adhere to the general rules of physics.
In modelling or MD, one attempts precisely to regenerate
reality by solving Newton’s equations of motion using well-
calibrated molecular force fields. Simulation or animation is
Table 1. Summary of different simulation or animation scenarios and the CPU
time taken to complete the calculation
Simulation examplePDB IDsTime
taken (s)a
Simple rotation about Z axis
Motion between two end-state conformers
Small-scale vibrational motions
Oligomerization (assembly/disassembly)
Ligand docking
NMR ensemble simulation
Protein folding/unfolding
4Q21
1A29 & 1CLL
1MYF_A
1C48
1A29 & TFP
1BQV
1A29
10
15
16
25
20
260
215
aTimes will vary according to server load and PDB file size.
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frequently employed by video game developers, cartoonists
and specialeffectsartists togenerateillusions ofmotion, speed
or impact. Rather than attempting to solve Newton’s equations
for every motion or event, most simulation specialists employ
rapidly calculable interpolations and ad hoc rules to generate
the necessary visual effect. This allows them to quickly gen-
erate the images needed for interactive game play or tight
movie release deadlines. By opting for animation over mod-
elling (i.e. mimicry over reality) we have been able to create
a very fast and flexible molecular animation tool. Although
the images and files generated by MovieMaker should not be
used to calculate or predict key molecular parameters, they
certainly could be of considerable use for many educational,
instructive or illustrative purposes by non-MD specialists.
We believe the animations produced by MovieMaker will
potentially allow the easy creation of dynamic web pages,
informative on line course notes and compelling PowerPoint
presentations.
ACKNOWLEDGEMENTS
Funding for this project was provided by the Protein
Engineering Network of Centres of Excellence (PENCE),
NSERC and Genome Prairie (a division of Genome Canada).
Funding to pay the Open Access publication charges for this
article was provided by Genome Prairie.
Conflict of interest statement. None declared.
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