Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure–function studies

Abstract

The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure–function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.

The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability

“…It not only validates the trustworthiness of the structural model but helps to shed light on the correlation between structure and function, on the dynamic behaviour of materials, and on their possible practical applications. Helliwell (2021) provides a wide variety of further examples.…”

Introduction to Materials Informatics

“…1,2 When working with experimental data and/or the simulation of experimental data, one must account for the nature of precision and accuracy in the measurement itself (e.g., specimen geometry, instrumental parameters, and the conditions of observation). 3 Incorporating all these factors can make evaluation and interpretation of spectroscopic profiles based on human-identifiable peaks difficult and convoluted. This is where machinelearning methods can be a powerful aid to probe structure-property relationships from experimental data.…”

Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines

“…In that way, the functions of protein machines are not only determined by their crystal structures at steady state, but also closely related to the conformational pathways connecting those states. Nowadays, the crystal structures at steady state are quite accessible through the application of cryo-electron microscopy, X-ray diffraction, or nuclear magnetic resonance [6]; however, the associated conformational pathways can hardly be characterized owing to the ephemerality and instability of intermediate states.…”

“…Scaled van der Waals energy term 5. Negative of a scaled charge-charge energy estimate of an unfolded protein 6. Polar energy contribution term 7.…”