My main interest is structural biology with emphasis on
the dynamics and flexibility of proteins and the correlation between
protein dynamics and function. My technical expertise is within the field
of protein NMR spectroscopy which is a particularly
well-suited method for the study of protein structure and dynamics at the
atomic level of detail. I also have an interest in NMR parameter
Structural biology is the study of biological processes at the molecular
and atomic level. Structural biology is closely related to biochemistry and
molecular biology and cannot be separated from these. Generally speaking,
structural biology is concerned with the characterizztion of the structure
and dynamics of biological macromolecules and the relation between
structure and dynamics on one side and biological function on the other
whereas biochemistry and molecular biology are concerned with the chemistry
of metabolic pathways and the DNA replication system, respectively. Some
important themes in structural biology include:
- Determination of and classification of the three-dimensional
structure of proteins by means of X-ray crystallography and NMR
- Elucidation of the catalytic mechanism of enzymes.
- Characterization of the ligand-binding sites on the surface of
- Determination of the interaction surfaces in protein-protein and
- Characterization of internal flexibility and dynamics of
biological macromolecules or complexes of biological macromolecules.
- Characterization of protein-protein and protein-solvent
interactions critical for protein stability and protein folding.
Allosteric enzymes where the binding of a signalling molecule results
in enzymatic activation, often in distant parts of the enzyme, have my
special interest. Here, the understanding of the changes in structure
and dynamics induced by the binding of the signalling molecule are
essential for understanding the function of the enzyme at the atomic
The activation of phosphoinositide 3-kinase (PI3K), which we are
investigating, is such an allosteric system. See
We are also investigating the dynamical properties and relationships
between dynamics and stability for human growth hormone. Humna growth
hormone (hGH) is a 22 kDa 4-helix bundle protein hormone essential for
normal growth during childhood and is an important pharmacophor in the
treatment of dwarfism. The flexibility-stability relationships for hGH
is particularly interesting because hGH exists in an unusually stable
partially folded state at acidic pH. We are currently investigating
the differences in flexibility of this state and the native state
in order to obtain insight into the interactions that govern protein
stability and folding.
Protein NMR spectroscopy is a rapidly evolving experimental method for
characterization of proteins in solution at the atomic level. The types of
information that can be obtained by NMR spectroscopic investigations of
Parameter estimation is concerned with the estimation of fundamental
physical paramters from experimental data. A simple example of parameter
estimation is linear regression. For more complex functional expressions,
non-linear least fitting is a useful method. For more specialized
estimation problems, special algorithms such as the linear prediction and
the maximum-entropy method may be particularly useful.
- Three-dimensional structure
- NMR spectroscopy allows the
determination of the three-dimensional structure at the atomic level of
small- to medium-sized proteins in solution and is an alternative or
complementary method to X-ray and neutron diffraction methods.
- Protein flexibility
- The dynamical properties of a protein can
be accessed through an analysis of NMR relaxation rates and provide
detailed information on the atomic level about the amplitude and the
timescale of dynamical processes in the protein.
- Conformational exchange
- Exchange between two conformational
states of a protein can be identified and the exchange-rate constant
can be estimated.
- Ionization constants
- Titration studies of a protein enable the
determination of ionization constants (acid dissociation constants)
for specific functional groups in the protein. It is thus possible to
focus on the specific functional groups relevant for function.
- Deuterium exchange
- Deuterium/hydrogen exchange rates for
labile (exchangable) protons can be measured and characterized on the
atomic level and provide information about the presence of hydrogen
bonds and about the lifetime of these bonds. In combination with
stopped-flow kinetic refolding experiments, deuterium/hydrogen
exchange measurements may provide detailed information about the
folding pathway of a protein.
- Rotational diffusion properties
- Carbon-13 and nitrogen-15 relaxation
measurements provide information about the overall rotational diffusion
properties of a protein and hence the shape and the rigidity of the
protein. In the study of proteins made up of two or more individually
folded domains, such measurements gives information about whether the
domains forms a rigid structure or are linked by flexible linkers.
- Relative orientation of protein domains
- Residual dipolar couplings
between nuclei which are close in space can be observed when proteins are
dissolved in dilute liquid crystal solvents. Such solvents are partially
aligned with the external magnetic field and causes a partial alignment of
the dissolved protein. The residual dipolar coupling constant between two
nuclei depends on the angle between the inter-nuclear vector and the
external magnetic field and if residual dipolar couplings can be measured
for a protein domain, the preferred orientation of the domain with respect
to the external magnetic field can be estimated. In proteins with two or
more domains, the orientation of the domains with espect to each other can
Parameter estimation is an integrated part of retrieving quantitative
information from NMR data.
Søren M. Kristensen, February 21, 2003