Future Prospects for Macromolecular Dynamics on 4th Generation Light Sources
Invited Speakers
- M. K. Kuimova, J. Dyer, M. W. George, D. C. Grills, J. Kelly, P. Matousek, A. W. Parker, X. Z. Sun, M. Towrie, A. M. Whelan, Chem. Commun. 2005, 1182
- M. K. Kuimova, A. J. Cowan, P. Matousek, A. W. Parker, X. Z. Sun, M. Towrie, M. W. George, Proc. Natl. Acad. Sci. USA 2006, 103, 2150
- “Photo-Induced Proton-Coupled Electron Transfer from Guanine to a Ruthenium Dipyridophenazine Complex Intercalated in a Double-Stranded Polynucleotide Monitored Directly using Picosecond Visible and Infrared Transient Absorption Spectroscopy” J. M. Kelly, C. Creely, G. W. Doorley, M. M. Feeney, B. Elias, C. Moucheron, A. Kirsch-de Mesmaeker, J. Dyer, D. C. Grills, M. W. George, P. Matousek, A. W. Parker, M. Towrie submitted
Martin Volk (University
of Liverpool, UK)
Fast Processes of α-Helix Folding
Folding and unfolding of α-helical peptides proceeds on the 100ns-time
scale and can be experimentally observed using fast laser-induced
temperature jumps; the ensuing structural relaxation of the
peptide can be followed by time-resolved IR-spectroscopy of the amide I’ band,
which is highly sensitive to secondary structure. Several examples
of recent results obtained in our lab will be described, including the use
of isotopic labelling, which allows the separate observation of labelled
and unlabeled peptide sections and thus provides dynamic information at
the residue level.
Luuk van Wilderen
(Vrije Universiteit, Amsterdam, The Netherlands)
Ultrafast infrared spectroscopy of Photoactive Proteins
To understand in detail how proteins can generate interpretable signals
about the physical conditions in our environment is a formidable
challenge. This challenge requires model systems, and in the natural sciences
photoactive proteins have generally been accepted as the most suitable models
available.
Photoactive Yellow Protein is studied with ultrafast visible
pump-mid infrared spectroscopy. A biologically productive state
is formed with a relatively low quantum yield of about 30%. The ideal tool
to investigate the underlying mechanism of this low efficiency is infrared
spectroscopy. Our results show with atomic detail what processes play a
key role in this process.
Kevin Kubarych
(University of Michigan, USA)
Towards real-time reaction dynamics in the condensed phase using triggered
multidimensional infrared spectroscopy
Recent developments in our laboratory have enabled a dramatic reduction of
the acquisition time of multidimensional infrared spectra by up to several
orders of magnitude. With only a few seconds needed to record a pulsed, Fourier
transform 2DIR spectrum, we will be able to incorporate a pump pulse to initiate
photochemical reactions and track these reactions in real time using non-equilibrium
chemical exchange. In particular, we expect non-equilibrium coherence transfer
top offer a new and highly sensitive probe of reaction dynamics. Initial investigations
will apply this transient 2DIR approach to simple photochemical reactions,
with the intention to tackle biologically relevant processes as the technique
matures.
Francois Haché
(École
Polytechnique, France)
Time-resolved circular dichroism
: application to the study of conformational changes in proteins
Circular dichroism (CD) is a very sensitive probe of molecular
conformation and we measure time-resolved CD in a pump-probe configuration
in order to access information on the conformational dynamics of
proteins. A set of experiments and calculations performed in
the visible on carbonmonoxy-myoglobin will be first presented.
We observe a transient CD (< 100 ps) that we attribute
to the squeezing of the proximal histidine following the heme doming.
Upgrading of the experiment towards the far-ultraviolet will then
be presented. In particular, a new technique based on the joint utilization
of a Babinet-Soleil compensator inserted in the probe path and of a mechanical
chopper on the pump will be described. This very user-friendly technique
proves to be well adapted to far-UV measurements. Finally, we will present
experimental projects aiming at observing the folding of model polypeptides.
Wojciech Gawelda (EPFL,
Lausanne, Switzerland)
Structural Dynamics Research with Ultrashort
X-rays
Electronic structure changes are at the origin of chemical reactivity, which drive the forming and breaking of bonds. Ultrafast X-ray Absorption Fine Structure spectroscopy (XAFS) delivers both the electronic and geometric transient structure changes, when interfaced with a femtosecond laser in a pump-probe scheme. In addition, XAFS methods are element-selective and can be applied to disordered bulk systems, in particular liquids. On the femtosecond time scale one would obtain a rather complete picture, via XAFS, since the propagation from a reaction center is limited to a few angstroms on these time scales.
We have recently recorded high-quality transient XAFS spectra at 3rd generation synchrotrons with currently < 100 ps temporal resolution, corresponding to the electron bunch width at the synchrotron. Examples of excited state structures of solvated coordination chemistry compounds and of short-lived atomic radicals in aqueous solution will be presented.
Extending these studies into the femtosecond time domain is straightforward
in concept, while pico- to nanosecond resolved studies still offers
a high potential for research on short-lived reaction intermediates,
whose structures can not be determined by other means. The continued efforts
using pulsed x-rays on the femto- to nanosecond time scales will be closely
linked to the simultaneous developments of novel photon sources, including
the 4GLS facility.
Sanford A. Asher and Alex Mikonen
Department of Chemistry, University of Pittsburgh
Pittsburgh, PA 15208 USA
P412-624-8570 asher@pitt.edu
UV Resonance Raman Elucidation of the Energy Landscape for Protein
Folding
We used UV resonance Raman excitation at ~200 nm to selectively enhance
the amide vibrations of the peptide backbone of a an α-helical peptide,
AP which consists of twenty one residues, 18 of which are ala and 3 arg.
We have examined the equilibrium structures through the approximately TM~30 °C
melting transition and utilized a nsec T-jump to examine the dynamics
of melting We demonstrated a quantitative correlation between a particular
Raman band, labeled as the amide III3 band and the Ramachandran Ψ angle.
From this correlation we are able to calculate the Ψ angle distribution as
a function of temperature. The Boltzmann relationship allows us to calculate
the Gibbs free energy as a function of temperature and Ψ angle. We find
that the α-helix melts to a mainly PPII like helix conformation.
We find that defective α-helix conformations melt before the pure α-helix.
Isotope editing studies and kinetic measurements allow us to understand the
complicated kinetics of melting. These studies explain anti-Arrhenius melting
behaviors previously observed for α-helix melting. We will compare
these results to the recent theoretical modeling for the transition
by the Madura group at Duquesne University.
Jon Waltho (University
of Sheffield)
Exploring photolytic triggers of protein folding
We have been developing chemical cross-linking reagents that perturb the
folded states of proteins, and can subsequenly be cleaved on a subpicosecond
timescale, hence triggering protein folding. The current generation of reagents
are based on aromatic sulphide chemistry and have been attached to three
proteins with very well determined folding characteristics, namely the N-terminal
domain of phosphoglycerate kinase, the d1 domain of CD2 and protein G. I
will discuss our progress in obtaining and characterising perturbed states
of these proteins and intial photolysis results.
Time-resolved Vibrational Spectroscopy of DNA#
Anthony W. Parker
Central laser Facility, CCLRC Rutherford Appleton Laboratory,
Chilton, Didcot, Oxfordshire
OX11 0QX, United Kingdom (a.w.parker@rl.ac.uk)
The photochemistry and the photophysics of nucleic acid bases and DNA is of fundamental importance in relation to understanding how nature protects the genetic code and the development of treatments for genetic disorders. The talk will give a brief review of the photo and radiation chemistry of the nucleic acid bases followed by an overview of our recent results. Two aspects will be covered: i) Direct damage studies using 205 and 266 nm to generate radical ions and photoexcited states respectively of various nucleic base sequences [1,2]. ii) Indirect damage studies via transient species formed by photo-excitation (400 nm) of [Ru(TAP)2(dppz)]2+ (1) (TAP = 1,4,5,8-tetraazaphenanthrene; dppz = dipyrido[3,2-a: 2’,3’-c] phenazine) when intercalated into [poly(dG-dC)]2. [3]
#This work is performed in collaboration with M. W. George, School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom and J. K. Kelly Department of Chemistry and Department of Physics, University of Dublin, Trinity College, Dublin 2, Ireland.
- Sanford Asher (University of Pittsburgh, USA) abstract »
- Wojciech Gawelda (EPFL, Lausanne, Switzerland) abstract »
- Francois Haché (École Polytechnique, France) abstract »
- David Klug (Imperial College, UK)
- Kevin Kubarych (University of Michigan, USA) abstract »
- Tony Parker (CCLRC, RAL) abstract »
- Martin Volk (University of Liverpool, UK) abstract »
- Jon Waltho (University of Sheffield) abstract »
- Luuk van Wilderen (Vrije
Universiteit, Amsterdam, The Netherlands) abstract »
The 4th Generation Light Source (4GLS) will provide extremely bright
sources of radiation covering the spectrum from soft X-ray to terahertz.
4GLS will use devices such as free electron lasers to provide laser
radiation in regions of the spectrum not accessible to conventional
lasers. It will provide very short pulses of radiation at high repetition
rates and will allow the combination of sources for pump-probe type
experiments.
One of the major applications of 4GLS will be the study of very fast dynamics in macromolecules; the aim of the meeting is to bring together the potential user community to hear presentations from world leaders in this area of science. There will be a series of presentations and also discussion sessions to allow the exchange of ideas and develop proposals for future experiments. The meeting will cover a range of spectroscopic techniques for investigating the dynamics of macromolecules in the sub-picosecond to microsecond time domain, including polarization methods (CD, TRORD), resonance raman, infrared, optical absorption, and 2D spectroscopy methods.
Programme
Available online » http://www.srs.ac.uk/meetings/4GLS_dynamics/programme.htm
Venue
Park Royal HotelPark Royal Hotel,
Stretton Road, Stretton, Warrington, WA4 4NS.
Registration
There will be a registration fee of £50 per delegate, which includes one night’s accommodation at the Park Royal HotelPark Royal Hotel, refreshments, and meals.
Online registration available here. Online registration available at http://conf.dl.ac.uk/register.asp?eventID=74.
Workshop Administrators
For questions regarding arrangements for the meeting
please contact a workshop administrator.
Alison Hannah
Tel: +44 (0)1925 603363, email: a.m.hannah@dl.ac.uk
Marie White
Tel: +44 (0)1925 603346, email: m.a.white@dl.ac.uk
