Probing the mechanoelastic mysteries of the HIV-1 capsid: a journey through theoretical and computational biophysics
Date
2024
Authors
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Publisher
University of Delaware
Abstract
Chapter 1 - Sub-cellular viral structures, namely protein capsids, are typically immense macromolecules which fulfill various critical roles in viral infection cycles; from protecting viral genomes, to communicating with host-cell machinery and, in the case of retroviruses, engendering chemistry such as reverse transcription, many fundamental aspects of the infection cycle depend upon these protein shells. Capsid structures, tiled from many copies of capsid protein (CA) subunits, possess macroscopic physical properties that emerge from many individual atomic interactions. Macroscopic properties such as balanced stability, flexibility, plasticity among interfaces and more are increasingly recognized as important determinants of successful infection. In order to gain molecular insights of capsid behavior, full-scale studies of native capsids are required. Here, two integrative modeling efforts are presented. First, a solid-state NMR-guided HIV-1 CA tubular assembly is described. Comprised solely of hexameric subunits, this system offers important insights on inter-hexameric interactions, and offers an information-rich ensemble of important structural features, such as host-factor binding domains. Next, an icosahedral (T=1) capsid of the Rous Sarcoma Virus (RSV) capsid is presented, which is comprised of solely CA pentamers. Through comparison with an RSV tubular assembly, our structure and subsequent analyses show how CA proteins accommodate pentameric vs. hexameric assemblies. ☐ Chapter 2 - Compartmentalization is a central theme in biology. Cells are composed of numerous membrane-enclosed structures, evolved to facilitate specific biochemical processes; viruses act as containers of genetic material, optimized to drive infection. Molecular dynamics simulations provide a mechanism to study biomolecular containers and the influence they exert on their environments; however, trajectory analysis software generally lacks knowledge of container interior versus exterior. Further, many relevant container analyses involve large-scale particle tracking endeavors, which may become computationally prohibitive with increasing system size. Here, a novel method based on 3-D ray casting is presented, which rapidly classifies the space surrounding biomolecular containers of arbitrary shape, enabling fast determination of the identities and counts of particles (e.g., solvent molecules) found inside and outside. The method is broadly applicable to the study of containers and enables high-performance characterization of properties such as solvent density, small-molecule transport, transbilayer lipid diffusion, and topology of protein cavities. The method is implemented in VMD, a widely used simulation analysis tool that supports personal computers, clouds, and parallel supercomputers, including ORNL’s Summit and Titan and NCSA’s Blue Waters, where the method can be employed to efficiently analyze trajectories encompassing millions of particles. The ability to rapidly characterize the spatial relationships of particles relative to a biomolecular container over many trajectory frames, irrespective of large particle counts, enables analysis of containers on a scale that was previously unfeasible, at a level of accuracy that was previously unattainable. ☐ Chapter 3 - Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell’s organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1’s life cycle. ☐ Chapter 4 - Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine. ☐ Chapter 5 - Growing evidence supports that the HIV-1 capsid is trafficked into host nuclei intact, thus gaining passage through the nuclear pore prior to reverse transcription induced dissambly. While these recent findings indicate that the HIV-1 capsid must possess elastic character to translocate through the relatively narrow nuclear pore complex (NPC), mechanoelastic properties of HIV-1 capsids have yet to be assessed. Further, the existence of hyperstable mutants which exhibit impaired or deficient nuclear entry adds intrigue to the idea of the capsid having evolved deformability through positive selection. Here, utilizing the dimensionality reduction technique presented in Chapter 4, we subject full scale HIV-1 capsids, wild type, hyperstable E45A and compensatory double mutant E45A/R132T, to simulated atomic force microscopy (AFM) experiments. We show that the capsid is a remarkably robust and elastic container that can accommodate extreme deformations prior to lattice failure. Further, we show that E45A-containing capsids have altered stiffness, suggesting that mechanical properties of capsids are related to successful nuclear entry. Finally, by characterizing the material response of the capsids studied, we show that E45A and R132T mutations not only affect mechanical stiffness, but material response as a whole, becoming less characteristically ductile and more brittle.
Description
Keywords
High performance computing, Retrovirology, Viruses, Capsid protein