Proteins are the molecular machinery of life. As nanomachines of metabolism, they are tirelessly active in every cell of our body, transporting, synthesizing, dividing and transforming substances. The ability of specific proteins to do their job is determined by the sequence of amino acids and their three-dimensional arrangement, but this in turn also depends on structural rearrangements deriving from environmental conditions.
To perform their function properly, structural changes are often important. These range from atomic reorientation to rearrangements of complete domains to enclose substrates, release products or reconfigure domains in complexes. Neutron Spin Echo Spectroscopy is a versatile tool to investigate these large scale movements in biomolecules on different length scales and to determine the timescale of the motions. The proteins can be examined in a D2O buffer solution, which is close to natural conditions. In addition, neutron scattering does not destroy proteins. In recent studies, we found large scale motions of complete domains in yeast alcohol dehydrogenase and phosphoglycerate kinase.
Intrinsically Unstructured Proteins and Disordered Regions
A large class of proteins does not exhibit a defined tertiary structure. These proteins may or may not have structured parts connected by disordered regions with a high degree of configurational freedom. This class challenges the traditional structure-function paradigm. The IUPs sometimes fold upon binding to an active configuration, e.g. in conjunction with other molecules. Understanding the dynamics is an important step in comprehending the structuring process prior to function, i.e. the dynamics of folding or function as an unstructured protein. Two approaches can be used to elucidate the underlying phenomena. Structured proteins can be partly unfolded (e.g. using temperature) to examine stable unfolded intermediates; intrinsically unfolded proteins can be examined directly. Taking an extreme case, a completely unstructured protein should behave as a stiff random polymer chain.
Structure of Protein Denatured States
Protein folding intermediates can be trapped chemically (denaturing agent, pH, ionic strength) as well as physically (temperature and pressure). Small Angle Neutron Scattering techniques allow access to protein structural intermediates as a function of temperature up to 120°C and as a function of pressure up to 5000 bar using the new high pressure set-up available at JCNS. The figure represents the Kratky plot showing scattered intensity for a myoglobin protein under chemical denaturing conditions. Besides the characterization of protein-folding intermediates, we are investigating the ligand binding effect on protein structure stability upon denaturation.
Protonation States of Proteins
Knowing the three-dimensional structure of a protein is a pre-requisite for understanding its function. Protein x-ray crystallography is a well-established tool to obtain structural information on proteins. However, with x-rays as probes, the position of hydrogen atoms can hardly be seen.
Here, neutron scattering on protein crystals opens up the possibility to locate hydrogen atoms even at moderate resolutions of 2 Å. For this reason, in collaboration with the FRM II in Garching, the BioDiff, a dedicated instrument for neutron protein crystallography is being built. An initial measurement of Bragg-reflections from a sperm whale myoglobin crystal with the CCD-detector of the BioDiff instrument is shown in the first picture on the left. The resulting protein structure is depicted in the picture on the right. Additional insights gained by using neutron protein crystallography includes, for example, the identification of unusual hydrogen bonds, the protonation state of side chains and the solvent structure around the protein, to name but a few.
T. E. Schrader