Periodic Reporting for period 1 - SimViRNA (Multiscale Simulations of HIV capsid assembly and RNA)
Reporting period: 2023-07-01 to 2025-06-30
This project aims to establish new approaches toward large-scale simulations of biomolecular systems. We concretely seek to develop bottom-up coarse-grained models for the immature HIV CA-SP1 lattice including protease dimers as well as for RNA systems. Proteolytic cleavage of the CA-SP1 junction is an essential process for disassembly of the immature HIV lattice and hence critical to HIV infectivity. How the protease processes the immature HIV lattice and hence triggers its disassembly has remained an open question of high therapeutical interest that we address in this project. To this purpose, we have performed structural modelling of the CA-SP1/protease complex and performed extensive atomistic simulations that we subsequently used to build large-scale coarse-grained models. Development of such models that exhibit realistic affinities between the binding partners is a major difficulty that we solved by designing a new machine-learning technique. In this way, we are able to simulate the immature HIV lattice that is composed of more than 3100 proteins exposed to protease dimers. Furthermore, we have implemented a bond-cleavage mechanism for the CA-SP1 junction in the presence of protease dimers. Performing reactive, coarse-grained simulations for this system, we aim to toward a mechanistic understanding of how proteases cooperatively disassemble the immature HIV lattice. Such insight is highly relevant for the design of new drugs inhibit HIV maturation through stabilization of the immature HIV lattice such as bevirimat.
Another objective of this project is the development of a hybrid atomistic/coarse-grained (MM/CG) model for RNA. Atomistic simulations of RNA macromolecules such as the ribosome are computationally too expensive. Long-range or cooperative effects, however, often play an important role in the conformational behavior of local domains. A pure coarse-grained representation, on the other hand, is of too low resolution to address fine-grained structural changes. Thus, we seek to resolve this dilemma by developing a hybrid model in which critical parts of the system are atomistically resolved, whereas the surrounding is described by a coarse-grained model. In this way, we seek to lay the methodological foundation for a new simulation standard, that facilitates the simulation of drug binding to RNA target-sites while capturing the macromolecular environment.
Another objective of this project is the development of a hybrid atomistic/coarse-grained (MM/CG) model for RNA. Atomistic simulations of RNA macromolecules such as the ribosome are computationally too expensive. Long-range or cooperative effects, however, often play an important role in the conformational behavior of local domains. A pure coarse-grained representation, on the other hand, is of too low resolution to address fine-grained structural changes. Thus, we seek to resolve this dilemma by developing a hybrid model in which critical parts of the system are atomistically resolved, whereas the surrounding is described by a coarse-grained model. In this way, we seek to lay the methodological foundation for a new simulation standard, that facilitates the simulation of drug binding to RNA target-sites while capturing the macromolecular environment.
Within this project, an experimental pdb-structure for a protease-peptide complex was used to build a structural model for a protease-dimer bound to a CA-SP1 site within the hexameric, immature HIV Gag-lattice. This represents one of the very first structural models for how proteases access the Gag-lattice for subsequent cleavage. Performing atomistic simulations starting from this complex structure, we have monitored that protease-binding induces structural changes in the lattice but not significant remodeling. To better understand large-scale remodeling as it occurs during HIV maturation, we have developed a coarse-grained model for this system. One of the main challenges here is to accurately describe affinities between different CA-SP1 monomers as well as between protease and CA-SP1, especially since binding/unbinding-events are difficult to sample for such large systems. We have resolved this issue by developing a new machine-learning method that represents a regularized version of relative entropy minimization. This new approach includes a quadratic bias on an empirical binding-affinity in its loss-function. In this way, it allows for accurate description of the complex structure as well as for the binding affinity. The method has been designed to guarantee maximum practicality, which means that no additional terms in the coarse-grained force fields or implementations in the simulation engine are required. Furthermore, we have demonstrated that hexameric CA-SP1 unit-models are transferable to simulate an entire immature HIV lattice. To simulate large-scale immature lattice remodeling triggered by proteolytic cleavages, we have developed a simulation routine in openmm that includes a CA-SP1 cleavage mechanism in the presence of protease. Application of these large-scale simulations allows us to characterize the disassembling-action by proteases that is critical to HIV maturation.
Most researchers perform coarse-grained simulations using existing top-down models, such as MARTINI. Developing a new coarse-grained model for the immature CA-SP1 lattice of HIV in a bottom-up approach, i.e. in consistency with atomistic data, is therefore clearly beyond state-of-the-art. In addition, molecular simulations usually also do not include reactions, such as proteolytic bond-cleavage. Implementation of such a mechanism into a simulation model is therefore also a very important extension over standard protocols. This approach is straightforwardly transferable also to other molecular systems, meaning that the newly developed approach and simulation protocol can serve as a template also for other researchers. Thus, it facilitates numerous future extensions that can have a high pharmaceutical impact. For instance, it allows one to also investigate how drugs can stabilize the immature lattice to undermine HIV maturation and hence devise new drug-targeting strategies.