ayout 1 - EMBL Grenoble

EMBL Hamburg
Macromolecular crystallography
Accurate modelling of biological processes depends on an intimate knowledge of the macromolecules
involved. The availability of models of the interacting components allows a deep understanding
of the basic processes that underlie human disease and all other cellular events. One
recent example is a basis for neurodegenerative pathologies provided by the structure of a stable
serpin dimer (Yamasaki et al., 2008, Nature).
Macromolecular structures are produced by a large number of independent scientists, all of whom
approach specific problems in their own manner. Methods are needed to establish objective structure
determination and quality assessment, which will impact further system-wide analysis. The
group’s major activity is development of novel approaches and software tools for high-throughput
3D structure determination and detailed interpretation of biological macromolecules and their
complexes. Specific attention is given to extension of the current limits of applicability of MX and
its use with complementary techniques.
Previous and current research
In MX, availability of comprehensive software packages has a major impact on structural biology.
Traditionally crystallographic model building is done by expert users with the aid of specialised
graphics software. The automation of this process, first exemplified in the ARP/wARP package
(Langer et al., 2008, Nature Protocols), was promptly followed by developments worldwide.
ARP/wARP has been used extensively for thousands of structure determinations and is often used
as a benchmark to evaluate the quality of electron density obtained by new methods; it has been integrated into many crystallographic software
pipelines as the default model-building engine. A wide spectrum of ARP/wARP functionalities (e.g. Hattne et al., 2008, Acta Cryst.) makes
the software particularly attractive to users.
We continue the developments of the automated structure determination pipeline AutoRickshaw (led by S. Panjikar in collaboration with the
Tucker group and Weiss team (pages 106 and 107)), which uses an artificial intelligence decision-making system (Manjasetty et al., 2008,
Proteomics). With the help of ARP/wARP and other software, AutoRickshaw produces
an interpretable electron density map and a partial structure shortly after data
acquisition. At our MX beamlines the users receive immediate feedback whether the
measured data are of sufficient quality for successful structure determination.
Our group has initiated the installation of the EMBL Hamburg advanced computational
facilities, where the in-house, beamline and external users can carry out 3D
structure determination remotely. These services for AutoRickshaw and particularly
ARP/wARP have become increasingly popular (see figure).
At the other end of the scale, we continue pushing the limits of model interpretation
at ultra-high resolution. Using quantum chemical calculations we were able to decipher
subtle changes in the active site residues upon substrate binding in Hydroxynitrile
lyase (Schmidt et al., 2008, J. Biol. Chem.). We showed that His235 of the catalytic
triad must be protonated in order for catalysis to proceed. We also detected considerable
pKa shifts that had been hypothesised earlier.
Future projects and goals
Victor S. Lamzin
PhD 1987, Moscow State
University.
Scientist, Inst. Biochemistry,
Russian Academy of
Sciences, Moscow, until
1991.
Postdoctoral research at
EMBL Hamburg until 1995;
Staff Scientist until 1997.
Group leader and Deputy
Head since 1997.
User numbers of the ARP/wARP and AutoRickshaw
remote computation facilities are increasing rapidly. In
2008 the facilities were used by more than 600 people,
and over 1,000 macromolecular structures were solved.
In the future we will witness the further integration of MX with complementary techniques, and the underlying methodology will face a number
of challenges. Crystalline samples are already obtained from increasingly complex biological systems and are becoming smaller and more
difficult to handle, with data harder to extract. The group’s activities will cast within the anticipated trend and aim at furthering the understanding
of molecular biological processes by increasing the amount of 3D information that can be obtained from biological macromolecules.
Selected references
Yamasaki, M., Li, W., Johnson, D.J. & Huntington, J.A. (2008).
Crystal structure of a stable dimer reveals the molecular basis of
serpin polymerization. Nature, 55, 1255-8
Hattne, J. & Lamzin, V.S. (2008). Pattern-recognition-based detection
of planar objects in three-dimensional electron-density maps. Acta
Crystallogr. D Biol. Crystallogr., 6, 83-82
Langer, G., Cohen, S.X., Lamzin, V.S. & Perrakis, A. (2008).
Automated macromolecular model building for X-ray crystallography
using ARP/wARP version 7. Nat. Protoc., 3, 1171-1179
Manjasetty, B.A., Turnbull, A.P., Panjikar, S., Bussow, K. & Chance,
M.R. (2008). Automated technologies and novel techniques to
accelerate protein crystallography for structural genomics.
Proteomics, 8, 612-625
Schmidt, A., Gruber, K., Kratky, C. & Lamzin, V.S. (2008). Atomic
resolution crystal structures and quantum chemistry meet to reveal
subtleties of hydroxynitrile lyase catalysis. J. Biol. Chem., 283,
21827-21836
101