Structure determination of protein binding to noncrystalline macromolecular assemblies such as plant cell walls (CWs) poses a significant structural biology challenge. CWs are loosened during growth by expansin proteins, which weaken the noncovalent network formed by cellulose, hemicellulose, and pectins, but the CW target of expansins has remained elusive because of the minute amount of the protein required for activity and the complex nature of the CW. Using solid-state NMR spectroscopy, combined with sensitivity-enhancing dynamic nuclear polarization (DNP) and differential isotopic labeling of expansin and polysaccharides, we have now determined the functional binding target of expansin in the Arabidopsis thaliana CW. By transferring the electron polarization of a biradical dopant to the nuclei, DNP allowed selective detection of 13 C spin diffusion from trace concentrations of 13 C, 15 N-labeled expansin in the CW to nearby polysaccharides. From the spin diffusion data of wild-type and mutant expansins, we conclude that to loosen the CW, expansin binds highly specific cellulose domains enriched in xyloglucan, whereas more abundant binding to pectins is unrelated to activity. Molecular dynamics simulations indicate short 13 C-13 C distances of 4-6 Å between a hydrophobic surface of the cellulose microfibril and an aromatic motif on the expansin surface, consistent with the observed NMR signals. DNP-enhanced 2D 13 C correlation spectra further reveal that the expansin-bound cellulose has altered conformation and is enriched in xyloglucan, thus providing unique insight into the mechanism of CW loosening. DNP-enhanced NMR provides a powerful, generalizable approach for investigating protein binding to complex macromolecular targets.carbohydrate-binding module | CBM A s part of the cell growth process, plants use expansins to induce wall stress relaxation, which creates the driving force for cell water uptake and consequent enlargement (1). Expansins were first discovered in studies of acid-stimulated growth of plant cells (2). Auxin, the classical plant growth hormone, rapidly stimulates growth in part by activating plasma membrane H + -ATPases, lowering wall pH, thereby activating expansins, which have a low pH optimum. Expansins mediate wall loosening not by lysis of the major polysaccharides of the growing cell wall (CW), but by weakening the noncovalent polysaccharide network that constitutes the load-bearing structure of the CW (3).Structural studies of the mechanism of expansin-mediated wall loosening have been hampered by the fact that active plant expansins are difficult to produce in recombinant expression systems. This obstacle was recently circumvented with the discovery of microbial expansins, which are readily expressed in Escherichia coli and enabled mutagenesis studies of the residues required for wall loosening and X-ray analysis of protein-oligosaccharide structures (4-6). These studies showed that expansins consist of two domains, D1 and D2, which present a nearly flat surface for binding to ce...

The heme group in paramagnetic (S ‫؍‬ 1͞2) ferricytochromes c typically displays a markedly asymmetric distribution of unpaired electron spin density among the heme pyrrole ␤ substituents. This asymmetry is determined by the orientations of the heme axial ligands, histidine and methionine. One exception to this is ferricytochrome c552 from Hydrogenobacter thermophilus, which has similar amounts of unpaired electron spin density at the ␤ substituents on all four heme pyrroles. Here, determination of the orientation of the magnetic axes and analysis of NMR line shapes for H. thermophilus ferricytochrome c 552 is performed. These data reveal that the unusual electronic structure for this protein is a result of fluxionality of the heme axial methionine. It is proposed that the ligand undergoes inversion at the pyramidal sulfur, and the rapid interconversion between two diastereomeric forms results in the unusual heme electronic structure. Thus a fluxional process for a metal-bound amino acid side chain has now been identified.

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

All-atom molecular dynamics simulations with explicit water solvent were used to investigate the microstructure and conformational dynamics of cellulose Iβ microfibrils as a function of microfibril length and cross-sectional size and shape. Cellulose microfibrils quickly develop a right-handed twist, which then remains stable over the entire 10 ns simulation time. The helical angle is independent of microfibril length and inversely proportional to its cross-sectional area, in accord with the expectations of continuum theory for an intrinsic chiral twist that is opposed by torsional shear. These calculations provide-to our knowledge-the first estimates of the shear modulus of a cellulose microfibril from MD simulations. The internal strains caused by this helical twist, propagated indefinitely along the microfibril axis, could be relaxed by periodic regions of amorphous structure along the axis of the cellulose microfibrils.

A model-free analysis of Pseudomonas aeruginosa ferricytochrome c(551) dynamics based on (15)N R(1), (15)N R(2), and [(1)H]-(15)N heteronuclear nuclear Overhauser effect data is reported. The protein backbone is highly rigid (< S(2)>=0.924+/-0.005) and displays little variation in picosecond-nanosecond time scale dynamics over the structure. The loop structure containing the axial methionine ligand (loop 3) displays anomalous rigidity, which is attributed to its high proline content. Also reported are protection factors calculated from hydrogen-exchange rates. These data reveal that loop 3 residues, including the axial methionine, are protected from exchange as a result of long-range hydrogen-bonding interactions. These results are contrasted with data reported for Saccharomyces cerevisiae iso-1-ferricytochrome c, which displays higher overall flexibility (< S(2)>=0.80+/-0.07), greater variation of dynamics as a function of structure, and low protection factors for loop 3. This analysis reveals that heme proteins with similar functions and topologies may display diverse dynamical properties.