Bond distances in polypeptide backbones depend on the local conformation

By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C—O and C—N) and those bonds centred on the Cαatom. All of these bond lengths indeed display a systematic variability in the ψ angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of Cαdistances on ψ is governed by interactions between the σ system of the Cαmoiety and the C—O π system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C—O and C—N distances is related to the strength of the interactions between the lone pair of the N atom and the C—O π* system, which is modulated by the ψ angle. The C—O and C—N distances are related but their trends are not strictly connected to peptide-bond planarity, although a correlation amongst all of these parameters is expected on the basis of the classical resonance model.

Structure of the recombinant BPTI/Kunitz-type inhibitorrShPI-1A from the marine invertebrateStichodactyla helianthus

The BPTI/Kunitz-type inhibitor family includes several extremely potent serine protease inhibitors. To date, the inhibitory mechanisms have only been studied for mammalian inhibitors. Here, the first crystal structure of a BPTI/Kunitz-type inhibitor from a marine invertebrate (rShPI-1A) is reported to 2.5 Å resolution. Crystallization of recombinantrShPI-1A required the salt-induced dissociation of a trypsin complex that was previously formed to avoid intrinsic inhibitor aggregates in solution. TherShPI-1A structure is similar to the NMR structure of the molecule purified from the natural source, but allowed the assignment of disulfide-bridge chiralities and the detection of an internal stabilizing water network. A structural comparison with other BPTI/Kunitz-type canonical inhibitors revealed unusual φ angles at positions 17 and 30 to be a particular characteristic of the family. A significant clustering of φ and ψ angle values in the glycine-rich remote fragment near the secondary binding loop was additionally identified, but its impact on the specificity ofrShPI-1A and similar molecules requires further study.

Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins

The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the φ/ψ angle of the residue [Berkholzet al.(2009),Structure,17, 1316–1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using theTNTrefinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in theRvalues. These tests support the value of revising refinement software to account for this new paradigm.

XRD2DScan: new software for polycrystalline materials characterization using two-dimensional X-ray diffraction

XRD2DScanis a Windows application for displaying and analyzing two-dimensional X-ray diffraction patterns collected with an area detector. This software allows users to take full advantage of diffractometers that are equipped with an area detector but that cannot readily process the information contained in diffraction patterns from polycrystalline materials.XRD2DScanhas many capabilities for generating different types of scans (2θ scan, ψ scan,dspacingversusψ angle), which allows users to extract the maximum amount of information from two-dimensional patterns. Analyses of multiple data files can be fully automated using batch processing. The use of the software is illustrated through several examples.

X-Ray Residual Stress Measurement in Films with Crystallographic Texture and Grain Shape

X-ray diffraction provides an easy and powerful method for measuring residual stress in thin films. However, nonlinearity of the d vs. sin2ψ relation can lead to the misinterpretation of results, especially when one of the measurements is made at low values of ψ relation for different combinations of ideal crystallographic textures and grain shapes are given. In all cases, a high ψ angle range exists where the d vs. sin2ψ relation in the low ψ angle range.