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Research interests

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 estimation methodology.

Structural biology

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:

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 level.

The activation of phosphoinositide 3-kinase (PI3K), which we are investigating, is such an allosteric system. See description.

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

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 protins include:
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 be determined.

Parameter estimation

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.

Parameter estimation is an integrated part of retrieving quantitative information from NMR data.


Søren M. Kristensen, February 21, 2003