Plenary Lecture

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

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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