No abstract

Combinatorial protein engineering provides powerful means for functional selection of novel binding proteins. One class of engineered binding proteins, denoted affibodies, is based on the three-helix scaffold of the Z domain derived from staphylococcal protein A. The Z SPA-1 affibody has been selected from a phagedisplayed library as a binder to protein A. Z SPA-1 also binds with micromolar affinity to its own ancestor, the Z domain. We have characterized the Z SPA-1 affibody in its uncomplexed state and determined the solution structure of a Z:Z SPA-1 protein-protein complex. Uncomplexed Z SPA-1 behaves as an aggregation-prone molten globule, but folding occurs on binding, and the original (Z) three-helix bundle scaffold is fully formed in the complex. The structural basis for selection and strong binding is a large interaction interface with tight steric and polar/nonpolar complementarity that directly involves 10 of 13 mutated amino acid residues on Z SPA-1. We also note similarities in how the surface of the Z domain responds by induced fit to binding of Z SPA-1 and Ig Fc, respectively, suggesting that the Z SPA-1 affibody is capable of mimicking the morphology of the natural binding partner for the Z domain.protein engineering ͉ protein-protein interactions ͉ molecular recognition ͉ NMR spectroscopy ͉ induced fit T here is an interest in generating novel classes of binding proteins that can be used as an alternative to immunoglobulins in various biochemical assays and biotechnological applications. To this end, carefully chosen protein domains can be used as framework structures for combinatorial protein engineering. Affibodies constitute a class of engineered binding proteins for which the three-helix bundle Z domain is used as a scaffold. The 58-aa residue Z domain is derived from one of five homologous domains (the B domain) in Staphylococcus aureus protein A (SPA). SPA binds strongly to the Fc region of immunoglobulins, and Z was originally developed as a stabilized gene fusion partner for affinity purification of recombinant proteins by using IgG-containing resins (1). The structure of a complex between the B domain of SPA and an Fc fragment shows that the binding surface consists of residues that are exposed on helices 1 and 2, whereas helix 3 is not directly involved in binding (2). Affibodies are selected from combinatorial libraries in which typically 13 residues at the Fc-binding surface of helices 1 and 2 are randomized. Specific binders to target proteins are then identified by biopanning the phage-displayed library against desired targets (3). Several Z-based affibodies with specific proteinbinding properties have in this way been developed and used as affinity tools in a number of applications (4-7).Structural studies of engineered protein-binding domains and their complexes are of interest for methods development in biotechnology as well as for basic studies of protein-protein interactions and the mechanisms of biomolecular recognition. Here we describe the (solution) structural and biophysic...

The McConnell equations combine the differential equations for a simple two-state chemical exchange process with the Bloch differential equations for a classical description of the behavior of nuclear spins in a magnetic field. This equation system provides a useful starting point for the analysis of slow, intermediate and fast chemical exchange studied using a variety of NMR experiments. The McConnell equations are in the mathematical form of an inhomogeneous system of first-order differential equations. Here we rewrite the McConnell equations in a homogeneous form in order to facilitate fast and simple numerical calculation of the solution to the equation system. The McConnell equations can only treat equilibrium chemical exchange. We therefore also present a homogeneous equation system that can handle both equilibrium and non-equilibrium chemical processes correctly, as long as the kinetics is of first-order. Finally, the same method of rewriting the inhomogeneous form of the McConnell equations into a homogeneous form is applied to a quantum mechanical treatment of a spin system in chemical exchange. In order to illustrate the homogeneous McConnell equations, we have simulated pulse sequences useful for measuring exchange rates in slow, intermediate and fast chemical exchange processes. A stopped-flow NMR experiment was simulated using the equations for non-equilibrium chemical exchange. The quantum mechanical treatment was tested by the simulation of a sensitivity enhanced 15N-HSQC with pulsed field gradients during slow chemical exchange and by the simulation of the transfer efficiency of a two-dimensional heteronuclear cross-polarization based experiment as a function of both chemical shift difference and exchange rate constants.

No abstract

Assignment of NMR spectra is a prerequisite for structure determination of proteins using NMR. The time spent on the assignment is comparatively long compared to that spent on other parts in the protein structure determination process, but it can be shortened by using either interactive or fully automated computer programs. To benefit from the advantages of both types of program we have developed a version of the interactive assignment program ANSIG to include automatized, yet user-supervised, routines. The new program includes tools for (i) semiautomatic sequential assignment, (ii) plotting of distances from PDB structure files directly in NMR spectra and (iii) statistical analysis of distance restraint violations with the possibility to directly zoom to violated NOEs in NOESY spectra.

No abstract

The five ribosomal P-proteins, denoted P0-(P1-P2)2, constitute the stalk structure of the large subunit of eukaryotic ribosomes. In the yeast Saccharomyces cerevisiae, the group of P1 and P2 proteins is differentiated into subgroups that form two separate P1A-P2B and P1B-P2A heterodimers on the stalk. So far, structural studies on the P-proteins have not yielded any satisfactory information using either X-ray crystallography or NMR spectroscopy, and the structures of the ribosomal stalk and its individual constituents remain obscure. Here we outline a first, coarse-grained view of the P1A-P2B solution structure obtained by a combination of small-angle X-ray scattering and heteronuclear NMR spectroscopy. The complex has an elongated shape with a length of 10 nm and a cross section of approximately 2.5 nm. 15N NMR relaxation measurements establish that roughly 30% of the residues are present in highly flexible segments, which belong primarily to the linker region and the C-terminal part of the polypeptide chain. Secondary structure predictions and NMR chemical shift analysis, together with previous results from CD spectroscopy, indicate that the structured regions involve alpha-helices. NMR relaxation data further suggest that several helices are arranged in a nearly parallel or antiparallel topology. These results provide the first structural comparison between eukaryotic P1 and P2 proteins and the prokaryotic L12 counterpart, revealing considerable differences in their overall shapes, despite similar functional roles and similar oligomeric arrangements. These results present for the first time a view of the structure of the eukaryotic stalk constituents, which is the only domain of the eukaryotic ribosome that has escaped successful structural characterization.

We present QSim, a program for simulation of NMR experiments. Pulse sequences are implemented and analyzed in QSim using a mouse driven interface. QSim can handle almost any modern NMR experiment, using multiple channels, shaped pulses, mixing, decoupling, phase-cycling and pulsed field gradients. Any number of spins with any spin quantum number can, in theory, be used in simulations. Relaxation is accounted for during all steps of pulse sequences and relaxation interference effects are supported. Chemical kinetics between any numbers of states can be simulated. Both classical and quantum mechanical calculations can be performed. The result of a simulation can be presented either as magnetization as a function of time or as a processed spectrum.