Biological Magnetic Resonance Data Bank.

The Biological Magnetic Resonance Data Bank (BMRB, https://bmrb.io) is the international open data repository for biomolecular nuclear magnetic resonance (NMR) data. Comprised of both empirical and derived data, BMRB has applications in the study of biomacromolecular structure and dynamics, biomolecular interactions, drug discovery, intrinsically disordered proteins, natural products, biomarkers, and metabolomics. Advances including GHz-class NMR instruments, national and trans-national NMR cyberinfrastructure, hybrid structural biology methods and machine learning are driving increases in the amount, type, and applications of NMR data in the biosciences. BMRB is a Core Archive and member of the World-wide Protein Data Bank (wwPDB).

Anomalous amide proton chemical shifts as signatures of hydrogen bonding to aromatic sidechains.

Hydrogen bonding between an amide group and the p-π cloud of an aromatic ring was first identified in a protein in the 1980s. Subsequent surveys of high-resolution X-ray crystal structures found multiple instances, but their preponderance was determined to be infrequent. Hydrogen atoms participating in a hydrogen bond to the p-π cloud of an aromatic ring are expected to experience an upfield chemical shift arising from a shielding ring current shift. We surveyed the Biological Magnetic Resonance Data Bank for amide hydrogens exhibiting unusual shifts as well as corroborating nuclear Overhauser effects between the amide protons and ring protons. We found evidence that Trp residues are more likely to be involved in p-π hydrogen bonds than other aromatic amino acids, whereas His residues are more likely to be involved in in-plane hydrogen bonds, with a ring nitrogen acting as the hydrogen acceptor. The p-π hydrogen bonds may be more abundant than previously believed. The inclusion in NMR structure refinement protocols of shift effects in amide protons from aromatic sidechains, or explicit hydrogen bond restraints between amides and aromatic rings, could improve the local accuracy of sidechain orientations in solution NMR protein structures, but their impact on global accuracy is likely be limited.

Merging NMR Data and Computation Facilitates Data-Centered Research.

The Biological Magnetic Resonance Data Bank (BMRB) has served the NMR structural biology community for 40 years, and has been instrumental in the development of many widely-used tools. It fosters the reuse of data resources in structural biology by embodying the FAIR data principles (Findable, Accessible, Inter-operable, and Re-usable). NMRbox is less than a decade old, but complements BMRB by providing NMR software and high-performance computing resources, facilitating the reuse of software resources. BMRB and NMRbox both facilitate reproducible research. NMRbox also fosters the development and deployment of complex meta-software. Combining BMRB and NMRbox helps speed and simplify workflows that utilize BMRB, and enables facile federation of BMRB with other data repositories. Utilization of BMRB and NMRbox in tandem will enable additional advances, such as machine learning, that are poised to become increasingly powerful.

Transmissive x-ray beam position monitors with submicron position- and submillisecond time resolution.

We present the development of fast transmissive center-of-mass x-ray beam position monitors with a large active area, based on a thinned position sensitive detector in both a duo- and a tetra-lateral variant. The detectors were tested at BESSY beamlines BL14.1, KMC-1, and KMC-2 and yielded signal currents of up to 3 microA/100 mA ring current at 10 keV photon energy using the monochromatic focused beam of BL14.1. The active area sizes were 1 x 1 and 3 x 3 mm(2) for the duo-lateral and 5 x 5 mm(2) for the tetra-lateral devices, with the duo-lateral detectors currently being available in sizes from 1 x 1 to 10 x 10 mm(2) and thicknesses between 5 and 10 microm. The presented detectors' thicknesses were measured to be 5 and 8 microm with a corresponding transmission of up to 93% at 10 keV and 15% at 2.5 keV. Up to a detection bandwidth of 10 kHz, the monitors provide submicron position resolution. For lower detection bandwidths, the signal-to-noise reaches values of up to 6 x 10(4) at 10 Hz, corresponding to a position resolution of better than 50 nm for both detector sizes. As it stands, this monitor design approach promises to be a generic solution for automation of state-of-the-art crystal monochromator beamlines.