CIFAR
RESEARCH BRIEF
A SERIES OF SUMMARIES OF INFLUENTIAL
RESEARCH STUDIES CONDUCTED BY CIFAR
PROGRAM MEMBERS
NOVEMBER 2016
MOLECULAR ARCHITECTURE OF LIFE
VISION STARTS WITH A SUPER-FAST
MOLECULAR DANCE
Rhodopsin, a pigment in the photoreceptor cells of the retina, absorbs light that enters the eye,
transforming it into the first chemical signal in the chain reaction of vision. Now researchers have
zeroed in on the molecular dynamics that make this ultrafast reaction possible.
FOCUS OF STUDY
Scientists have long explored the chemistry that makes
vision possible. But the primary chemical reaction
underlying vision occurs so fast that details about
what happens at the molecular level have remained
elusive. This experiment investigated what particular
movements the retinal molecule makes when light hits
it, and how these molecular vibrations work in sync to
initiate the first step in the chain reaction of vision.
BACKGROUND
The body uses a type of molecule called rhodopsin
to detect light that enters the eye. The surfaces
of the photoreceptor cells in the retina are dense
with rhodopsin molecules embedded in the plasma
membranes. Each rhodopsin molecule consists of the
protein opsin and the chromophore retinal.
When light hits the retinal chromophore, it causes the
molecule to isomerize, changing its shape and the
shape of the entire rhodopsin molecule along with it.
In this new state, rhodopsin can interact with other
proteins in the photoreceptor cell, kick-starting the
visual signaling cascade that ultimately sends a neural
impulse to the brain.
During this key isomerization reaction, the retinal
molecule flips like a switch from a cis- to a transorientation around its carbons 11 and 12, which are
connected by a double bond .
This flip is incredibly fast. Because of its speed,
previous research has been unable to identify the
vibrations of the molecule that enable it. Chemical
reactions like this one occur as a result of movements
of the molecule that bring particular atoms into
contact at just the right time, causing them to react to
each other.
This experiment demonstrates that the
primary chemical reaction of vision
happens much faster than previously
thought, and reveals the molecular
dynamics that cause it.
These molecular movements can include twisting and
stretching of the bonds between the molecule’s atoms,
and many other types of movement. Each molecular
movement emits a vibration that can be detected.
However, over the isomerization reaction of retinal, the
molecule emits many different vibrations caused by
many different movements of the molecule. Previous
experiments didn’t examine the reaction on a short
enough timescale to distinguish which of these
vibrations were involved in the reaction and which
were background noise.
This study used ultrafast heterodyne-detected transientgrating spectroscopy, exciting the retinal in rhodopsin
with pulses of light to examine the isomerization
reaction on a shorter timescale than ever before.
FINDINGS
The researchers were able to characterize
what happens to the retinal molecule during its
isomerization at an unprecedented level of detail. By
observing the event to a finer degree than previous
studies, they captured a better picture of how long the
reaction takes and pinpointed the particular vibrational
modes that make it happen.
The researchers found evidence that the isomerization
of retinal is a vibrationally coherent photochemical
process with three particular vibrations that occur
b
simultaneously in different parts of the molecule. These
oscillate in sync to cause a single, ultrafast molecular
flip.
They also found that the isomerization event happens
much faster than previously thought, on a timescale
of about 30 femtoseconds — that’s 30 millionths of
a billionth of a second. Previous experiments had
estimated the reaction to occur over about 200
femtoseconds.
300
Amplitude (a.u.)
200
17,750 cm -1
100
0
-100
20,000 cm -1
-200
- 100
0
100
200
300
400
500
Probe delay (fs)
Figure 1: [from figure 2b] The absorption band for isomerized retinal appears within about 30 femtoseconds after the probe light pulse of
17,750 cm−1 has been applied.
The researchers concluded that the signals detected
at 200 femtoseconds in previous studies had been due
to the retinal becoming “vibrationally hot” during its
recovery after isomerization, not to the isomerization
reaction itself.
Three main reactive nuclear dynamics within the
molecule appeared to drive the reaction. These
movements were local stretching of the C11=C12 double
bond, HOOP wags in and out of the local polyene
chain plane by the C11 and C12 hydrogens and torsional
vibration around the C11=C12 double bond.
METHODOLOGY
The researchers used ultrafast heterodyne-detected
transient-grating spectroscopy to observe the
isomerization of retinal in a sample of bovine
rhodopsin that had been isolated from frozen bovine
retinae.
They used an anamorphic-pumped non-collinear
optical parametric amplifier (NOPA) to generate
pulses of light in the blue-green spectrum that lasted
approximately 11 femtoseconds each.
Four ultrashort pulses of light were shot at the
sample to excite its molecules. This caused the
retinal to isomerize, and enabled the researchers
to pick up the resulting resonances emitted by the
retinal molecules.
The first two pulses of light were sent at the same
time, striking the retinal sample simultaneously
adjacent to one another and causing a standing
wave interference pattern. The third pulse was
shot to probe this interference pattern and a larger
fourth pulse was used to detect the resulting
interference.
Ultrashort pulses of blue-green light
were used to observe the isomerization
of the retinal molecule when it’s
exposed to light — a key chemical
process that drives vision — at a level
of detail never before observed.
The experiment relied on the principle that as the
retinal molecules became excited by the light pulses,
their vibrations would alter an interference pattern
these pulses created. Each type of vibration in the
molecule that occurred would modulate the detected
signal differently depending on its location, timing and
type.
Because the transient-grating spectroscopy picked
up many molecular vibrations at once, the signal was
separated using Fourier filtering and time-domain
analysis. The different types of vibrations were then
identified and assigned to particular molecular
movements at particular times.
The three major types of molecular vibrations were
found to occur together at 30 femtoseconds in an
unusually coherent manner.
IMPLICATIONS
This experiment has uncovered a detailed profile of
the nuclear dynamics that happen in the primary
chemical reaction of vision, providing a more complete
explanation of how vision works at the molecular level.
The experiment revealed the inner workings of
an important class of receptors called G-proteincoupled receptors. Rhodopsin is one type of these.
G-protein-coupled receptors are present in many
systems throughout the body, transmitting a wide
variety of chemical signals including hormones and
neurotransmitters.
Dysfunctional G-protein-coupled receptors are
implicated in diseases that cause vision loss, heart
failure, metabolic syndrome, schizophrenia, epilepsy,
pain, cancer, fertility disorders and many other
conditions. An estimated 50 per cent of current drugs
are related to diseases that involve G-protein-coupled
receptors.
A clearer understanding of how these receptors
efficiently recognize and relay chemical signals
broadens our understanding of this major component
of human physiology.
REFERENCE
Local vibrational coherences drive the primary photochemistry of vision. Philip J. M. Johnson, et al., Nature
Chemistry 7, 980–986 (2015).
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