A method for intuitively extracting macromolecular dynamics from structural disorder

Macromolecular dynamics manifest as disorder in structure determination, which is subsequently accounted for by displacement parameters (also called temperature factors, or B-factors) or alternate conformations. Though B-factors contain detailed information about structural dynamics, they are the total of multiple sources of disorder, making them difficult to interpret and thus little-used in structural analysis. We report here an analytical approach for decomposing molecular disorder into a parsimonious hierarchical series of contributions, providing an intuitive basis for quantitative structural-dynamics analysis. We demonstrate the decomposition of disorder on example SARS-CoV-2 and STEAP4 structures, from both crystallographic and cryo-electron microscopy data, and reveal how understanding of the macromolecular disorder leads to deeper understanding of molecular motions and flexibility, and suggests hypotheses for molecular mechanisms.

Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules

Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope which can be utilized for the study of macromolecular complexes, including the multi-component protein–DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology.

Effect of Dendritic Side Groups on the Mobility of Modified Poly(epichlorohydrin) Copolymers

The macromolecular dynamics of dendronized copolymer membranes (PECHs), obtained by chemical modification of poly(epichlorohydrin) with the dendron 3,4,5-tris[4-(n-dodecan-1-yloxy)benzyloxy] benzoate, was investigated. In response to a thermal treatment during membrane preparation, these copolymers show an ability to change their shape, achieve orientation, and slightly crystallize, which was also observed by CP-MAS NMR, XRD, and DSC. The phenomenon was deeply analyzed by dielectric thermal analysis. The dielectric spectra show the influence of several factors such as the number of dendritic side groups, the orientation, their self-assembling dendrons, and the molecular mobility. The dielectric spectra present a sub-Tg dielectric relaxation, labelled as γ, associated with the mobility of the benzyloxy substituent of the dendritic group. This mobility is not related to the percentage of these lateral chains but is somewhat hindered by the orientation of the dendritic groups. Unlike other less complex polymers, the crystallization was dismantled before the appearance of the glass transition (αTg). Only after that, clearing transition (αClear) can be observed. The PECHs were flexible and offered a high free volume, despite presenting a high degree of modifications. However, the molecular mobility is not independent in each phase and the self-assembling dendrons can be eventually fine-tuned according to the percentage of grafted groups.

Construction of a 3-color prism-based TIRF microscope to study the interactions and dynamics of macromolecules

Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for realtime visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and oper-ation of a 3-color prismTIRF microscope which can be utilized for the study macromolecular complexes, including the multi-component protein-DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology to a broader spectrum of scientific questions.

A method for intuitively extracting macromolecular dynamics from structural disorder

Macromolecular dynamics manifest as disorder in structure determination, which is subsequently accounted for by displacement parameters (also called temperature factors, or B-factors) or alternate conformations. Though B-factors contain detailed information about structural dynamics, they are the total of multiple sources of disorder, making them difficult to interpret and thus little-used in structural analysis. We report here an approach for decomposing molecular disorder into a parsimonious hierarchical series of contributions, providing an intuitive basis for quantitative structural-dynamics analysis. We demonstrate the decomposition of disorder on example SARS-CoV-2 and STEAP4 structures, from both crystallographic and cryo-electron microscopy data, and reveal how understanding of the macromolecular disorder leads to deeper understanding of molecular motions and flexibility, and suggests hypotheses for molecular mechanisms.

Molecular Skin Surface-Based Transformation Visualization between Biological Macromolecules

Molecular skin surface (MSS), proposed by Edelsbrunner, is a C2 continuous smooth surface modeling approach of biological macromolecules. Compared to the traditional methods of molecular surface representations (e.g., the solvent exclusive surface), MSS has distinctive advantages including having no self-intersection and being decomposable and transformable. For further promoting MSS to the field of bioinformatics, transformation between different MSS representations mimicking the macromolecular dynamics is demanded. The transformation process helps biologists understand the macromolecular dynamics processes visually in the atomic level, which is important in studying the protein structures and binding sites for optimizing drug design. However, modeling the transformation between different MSSs suffers from high computational cost while the traditional approaches reconstruct every intermediate MSS from respective intermediate union of balls. In this study, we propose a novel computational framework named general MSS transformation framework (GMSSTF) between two MSSs without the assistance of union of balls. To evaluate the effectiveness of GMSSTF, we applied it on a popular public database PDB (Protein Data Bank) and compared the existing MSS algorithms with and without GMSSTF. The simulation results show that the proposed GMSSTF effectively improves the computational efficiency and is potentially useful for macromolecular dynamic simulations.