Plenary
Lecture
Structure and Dynamics Elucidation of Biopolymers from
Constrained QM/MM Calculations - From NMR Chemical Shifts
to Structure and Dynamics
Dr. Ulrich
Sternberg
Karlsruhe Institute of Technology
POB 3640, D-76021 Karlsruhe
Germany
E-mail:
Ulrich.Sternberg@ibg.fzk.de
Abstract: NMR is a major
source of information on the
structure and dynamics of
bio-molecules. New computational
methods are presented that use NMR
data as target functions for
structure elucidations. It can be
shown that chemical shifts can be
used for the 3D structure
refinement of proteins and other
biopolymers. Additionally the
orientation and dynamics can be
investigated from molecular
dynamics (MD) simulations with
orientational constraints.
Prerequisites are a force field,
an effective method for computing
structure dependent atomic
charges, and a very fast method
for the computation of chemical
shifts (bond polarization theory –
BPT). Using the COSMOS-NMR hybrid
force field with semi-empirical
atomic charges and chemical
shifts, the calculations can be
performed in every step of an MD
simulation or geometry
optimization. To the energy,
provided by the force field,
pseudo energies are added. They
depend on the differences between
experimental and calculated
chemical shifts. In addition to
the energies pseudo forces have to
be computed. This requires
derivatives of the chemical shifts
with respect to the coordinates.
The pseudo forces are analytically
derived from the integral
expressions of the bond
polarization theory (BPT).
In the case of liquid state NMR
structure investigations of
proteins, 13C and 15N chemical
shift constraints can be added to
obtain accurate structure data for
the main chain and side chain
carbons. This method was first
applied to a zinc complex of a
synthetic pseudo-peptide and to
membrane active peptides. In the
case of proteins chemical shifts
can be used to find families of
structures that represent best the
conformer distribution in
solution.
Chemical shifts constraints are
beneficial especially in solid
state structure investigations. In
case of silk and cellulose,
crystal structures have been
computed that fulfil both the
13C-NMR chemical shift and the
X-ray constraints. It was shown
that for the newly refined
structures the calculated chemical
shift tensor elements match the
experimental values very well.
Since biopolymers like silk give
poorly defined X-ray patterns,
solid state NMR investigations can
be used to obtain better resolved
crystal structures.
Membrane and other solid state NMR
investigations exploit the
tensorial character of the NMR
parameters. These tensors can be
used in MD simulation as
orientational constraints to
produce a detailed picture of
molecular motion and order.
Brief Biography of the Speaker:
20.11.1946: Born in Brandenburg/Havel,
Germany.
1965-1970: Studies in chemistry at
the Humboldt University Berlin.
1975: Thesis in Theoretical
Chemistry on the calculation of
magnetic susceptibilities and
nuclear shieldings.
1975-1978: Development of the
graphics for a computer system
that predicts chemical reactions.
1976-1988: Research and lecturing
at the physics department of the
Fiedrich-Schiller University Jena.
Development of the Bond
Polarization Theory (BPT).
1988: Thesis B on BPT chemical
shift calculations, facultas
docendi and Dr. sc.
1991: Habilitation for applied
physics.
Lectures for Physicists on „Atoms,
Molecules and Quantum Theory“
1992: Privatdozent at the Physics
Department of the Fiedrich-Schiller
University Jena
1994: The software COSMOS (NMR
Molecular Modelling) wins the
“European Academic Software
Award“.
2001: Group leader of the NMR
facility at Physics Department.
2002: Development of computational
methods at the Bio-NMR group of
the Research Centre Karlsruhe
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