Xiongwu Wu

By Xiongwu Wu and Bernard R. Brooks

Part of the book: Fourier Transform

By Xiongwu Wu and Bernard R. Brooks

Electron microscopy (EM) and electron tomography (ET) have found extensive application to probe structural and dynamic properties of macromolecular assemblies. As an important complementary to X-ray and NMR in atomic structural determination, EM has reached a milestone resolution of 2.2Å, enough for understanding atomic interactions, interpreting mechanism of functions, and for structure-based drug design. This work describes approaches to derive structural information from EM/ET images and methods to study dynamics of macromolecular systems using EM/ET images as starting or ending targets. For low-resolution EM/ET maps, X-ray or NMR atomic structures of molecular components are needed to reduce the number of degrees of uncertainty. Depending on the resolution of EM/ET maps and the conformational differences from the X-ray or NMR structures, either rigid fitting or flexible fitting is used to obtain atomic structures. To illustrate the procedures of the atomic structure derivation, this work describes the core-weighted grid-threading Monte Carlo (CW-GTMC) rigid fitting and the map-restrained self-guided Langevin dynamics (MapSGLD) flexible fitting methods. Their applications are highlighted with four examples: architecture of an icosahedral pyruvate dehydrogenase complex, dynamics of a group II chaperonin, high-resolution structure of the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside, and the mechanism of kinesin walking on microtube.

Part of the book: Modern Electron Microscopy in Physical and Life Sciences

By Xiongwu Wu and Bernard R. Brooks

Protein-protein docking is a molecular modeling strategy to predict biomolecular complexes and assemblies. Traditional protein-protein docking is performed at atomic resolution, which relies on X-ray and NMR experiments to provide structural information. When dealing with biomolecular assemblies of millions of atoms, atomic description of molecular objects becomes very computational inefficient. This article describes a development work that introduces map objects to molecular modeling studies to efficiently derive complex structures through map-map conformational search. This method has been implemented into CHARMM as the EMAP command and into AMBER in its SANDER program. This development enables molecular modeling and simulation to manipulate map objects, including map input, output, comparison, docking, etc. Through map objects, users can efficiently construct complex structures through protein-protein docking as well as from electron microscopy maps according to low map energies. Using a T-cell receptor (TCR) variable domain and acetylcholine binding protein (AChBP) as example systems, we showed the application to model an energetic optimized complex structure according to a complex map. The map objects serve as a bridge between high-resolution atomic structures and low-resolution image data.

Part of the book: Molecular Docking and Molecular Dynamics