Symmetry in normal modes and its strong dependence on symmetry in structure

Structure-based insights into the mechanism of nucleotide import by HIV-1 capsid

Nucleotide import is critical to the reverse transcription and thus a key step in the life cycle of HIV-1 virus. In this work, boosted by the recently determined atomic structure of the whole HIV-1 capsid and our understanding of its dynamics, we carry out a computational structure-based study of the mechanism of nucleotide import by HIV-1 capsid. Our analysis reveals a number of novel insights into the mechanism. Specifically, our structure analysis indicates that arginine 18 side chains use a bind-translocate-release mechanism to bind and guide the long nucleotide to pass through the arginine ring before releasing it into the capsid. We discover that LYS 25 plays a critical role in defining the directionality of the transport, in facilitating the disassociation of nucleotides from the arginine ring, and in relaying them further into the interior of the capsid. We predict that mutations of LYS 25 to other residues, assuming that they still result in viable viruses, should reverse the directionality of the transport and significantly lower the infectivity.

A time and memory efficient recipe for fast normal mode computations of complexes with icosahedral symmetry

With the recent breakthroughs in experimental technologies, structure determination of extremely large assemblies, many with icosahedral symmetry, has been rapidly accelerating. Computational studies of their dynamics are important to deciphering their functions as well as to structural refinement but are challenged by their extremely large size, which ranges from hundreds of thousands to even millions of atoms. Group theory can be used to significantly speed up the normal mode computations of these symmetric complexes, but the derivation is often obscured by the complexity of group theory and consequently is not widely accessible. To address this problem, this work presents an easy recipe for normal mode computations of complexes with icosahedral symmetry. The recipe details how the Hessian matrix in symmetry coordinates can be constructed in a few easy steps of matrix multiplications, without going through the complexity of group theory. All the "ingredient" matrices required in the recipe are fully provided in the Supplemental Information for easy reproduction. The work is timely considering the expected large in-flux of many more icosahedral assemblies in the near future. The recipe uses a minimum amount of memory and solves the normal modes in a significantly reduced amount of time, making it feasible to perform normal mode computations of these assemblies on most computer systems.

All-atom normal mode dynamics of HIV-1 capsid

Dynamics of biomolecular assemblies offer invaluable insights into their functional mechanisms. For extremely large biomolecular systems, such as HIV-1 capsid that has nearly 5 millions atoms, obtaining its normal mode dynamics using even coarse-grained models can be a challenging task. In this work, we have successfully carried out a normal mode analysis of an entire HIV-1 capsid in full all-atom details. This is made possible through our newly developed BOSE (Block of Selected Elasticity) model that is founded on the principle of resonance discovered in our recent work. The resonance principle makes it possible to most efficiently compute the vibrations of a whole capsid at any given frequency by projecting the motions of component capsomeres into a narrow subspace. We have conducted also assessments of the quality of the BOSE modes by comparing them with benchmark modes obtained directly from the original Hessian matrix. Our all-atom normal mode dynamics study of the HIV-1 capsid reveals the dynamic role of the pentamers in stabilizing the capsid structure and is in agreement with experimental findings that suggest capsid disassembly and uncoating start when the pentamers become destabilized. Our results on the dynamics of hexamer pores suggest that nucleotide transport should take place mostly at hexamers near pentamers, especially at the larger hemispherical end.

Supramolecular assemblies are large biomolecular complexes composed of hundreds or even thousands of protein chains. They function as molecular machines or as large containers that store or facilitate the chemical reactions of other molecules. Whatever they do, their functional mechanisms are tightly linked to their structures and intrinsic dynamics. Recently, due to breakthroughs in experimental techniques, many supramolecular assemblies have been determined, such as the capsid of human immunodeficiency virus (HIV) that is composed of nearly 5 millions of atoms. Computational studies of these systems are challenging due to their extremely large sizes. In this work, we have successfully carried out a dynamics study of an entire HIV capsid in full all-atom details. Our study reveals new insights into the dynamics of the N-terminal loops, the stabilizing role of the pentamers, and where the nucleotide transport may take place.