T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles

T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl

Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases

The bacterial second messenger cyclic di-3′,5′-guanosine monophosphate (c-di-GMP) is a key regulator of bacterial motility and virulence. As high levels of c-di-GMP are associated with the biofilm lifestyle, c-di-GMP hydrolysing phosphodiesterases (PDEs) have been identified as key targets to aid development of novel strategies to treat chronic infection by exploiting biofilm dispersal. We have studied the EAL signature motif-containing phosphodiesterase domains from the Pseudomonas aeruginosa proteins PA3825 (PA3825EAL) and PA1727 (MucREAL). Different dimerisation interfaces allow us to identify interface independent principles of enzyme regulation. Unlike previously characterised two-metal binding EAL-phosphodiesterases, PA3825EAL in complex with pGpG provides a model for a third metal site. The third metal is positioned to stabilise the negative charge of the 5′-phosphate, and thus three metals could be required for catalysis in analogy to other nucleases. This newly uncovered variation in metal coordination may provide a further level of bacterial PDE regulation

The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase

The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS). TRPS uses a set of α/β–dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand–bound conformations. Our simulations also revealed that the α/β–dimeric unit stabilizes the substrate–protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function

High-brightness self-seeded X-ray free-electron laser covering the 3.5 keV to 14.6 keV range

A self-seeded X-ray free-electron laser (XFEL) is a promising approach to realize bright, fully coherent free-electron laser (FEL) sources in the hard X-ray domain that have been a long-standing issue with longitudinal coherence remaining challenging. At the Pohang Accelerator Laboratory XFEL, we have demonstrated a hard X-ray self-seeded XFEL with a peak brightness of 3.2 �� 1035 photons s?1 mm?2 mrad?2 0.1% bandwidth (BW)?1 at 9.7 keV. The bandwidth (0.19 eV) is about 1/70 times as wide (close to the Fourier transform limit) and the peak spectral brightness is 40 times higher than in self-amplified spontaneous emission (SASE), with substantial improvements in the stability of self-seeding and noticeably suppressed pedestal effects. We could reach an excellent self-seeding performance at a photon energy of 3.5 keV (lowest) and 14.6 keV (highest) with the same stability as the 9.7 keV self-seeding. The bandwidth of the 14.6 keV seeded FEL was 0.32 eV, and the peak brightness was 1.3 �� 1035 photons s?1 mm?1 mrad?1 0.1%BW?1. We show that the use of seeded FEL pulses with higher reproducibility and a cleaner spectrum results in serial femtosecond crystallography data of superior quality compared with data collected using SASE mode. ? 2021, The Author(s), under exclusive licence to Springer Nature Limited part of Springer Nature.11Nsciescopu

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching.

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born-Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3](2+) compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersion of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.Etude femtoseconde rayons X et optique de la dynamique ultrarapide de photocommutation de matériaux moléculaires magnétique