Session F53: Biological Materials Self-Assembly

Amyloid fibrils: formation, replication, and physics behind them

The assembly of normally soluble proteins into long fibrils, known as amyloids, is associated with a range of pathologies, including Alzheimer's and Parkinson's diseases. A large number of structurally unrelated proteins form this type of fibrils, and we are in a pursuit of physical principles that underlie the amyloid formation and propagation. We show that small disorders oligomers, which are increasingly believed to be the prime cause for cellular toxicity, serve as nucleation centers for the fibril formation. We then relate experimentally measurable kinetic descriptors of amyloid aggregation to the microscopic mechanisms of the process. Once formed, amyloid fibrils can catalyse the formation of new oligomers and fibrils in a process that resembles self-replication. By combining simulations with biosensing and kinetic measurements of the aggregation of Alzheimer's A$\beta $ peptide, we propose a mechanistic explanation for the self-replication of protein fibrils, and discuss its thermodynamic signature. Finally, we consider the design of possible inhibitors of the fibril self-replication process. Mechanistic understandings provided here not only have implications for future efforts to control pathological protein aggregation, but are also of interest for the rational assembly of bionanomaterials, where achieving and controlling self-replication is one of the unfulfilled goals.   

Coarse-grained models of key self-assembly processes in HIV-1

Computational molecular simulations can elucidate microscopic information that is inaccessible to conventional experimental techniques. However, many processes occur over time and length scales that are beyond the current capabilities of atomic-resolution molecular dynamics (MD). One such process is the self-assembly of the HIV-1 viral capsid, a biological structure that is crucial to viral infectivity. The nucleation and growth of capsid structures requires the interaction of large numbers of capsid proteins within a complicated molecular environment. Coarse-grained (CG) models, where degrees of freedom are removed to produce more computationally efficient models, can in principle access large-scale phenomena such as the nucleation and growth of HIV-1 capsid lattice. We report here studies of the self-assembly behaviors of a CG model of HIV-1 capsid protein, including the influence of the local molecular environment on nucleation and growth processes. Our results suggest a multi-stage process, involving several characteristic structures, eventually producing metastable capsid lattice morphologies that are amenable to subsequent capsid dissociation in order to transmit the viral infection.   

Chemically-controlled Assembly of Functional Protein Architectures

Proteins represent the most versatile building blocks available to living organisms or the laboratory scientist for constructing functional materials and molecular devices. Underlying this versatility is an immense structural and chemical heterogeneity that renders the programmable self-assembly of proteins an extremely challenging design task. To circumvent the challenge of designing extensive non-covalent interfaces for controlling protein self-assembly, we have endeavored to use chemical bonding strategies based on fundamental principles of inorganic and supramolecular chemistry. These strategies have resulted in discrete or infinite, 1-, 2- and 3D protein architectures that display high structural order over large length scales (yet are dynamic/adaptive and stimuli-responsive) and possess new emergent chemical/physical properties.   

Simulations of self-assembling DNA

The ability of complementary sequences of DNA to self assemble has been harnessed by DNA nanotechnology to create an extremely impressive array of DNA nanostructures. Even now, over ten years since Rothemund's first smiley-faced DNA origami appeared on the cover of Nature, it seems remarkable that such complex structures can form so easily. As probing the mechanisms of assembly is experimentally difficult, molecular simulations can potentially provide important microscopic insights. In this talk, I will describe our attempts to uncover the fundamentals of DNA self-assembly using oxDNA, a coarse-grained model of DNA developed in Oxford. Starting from a consideration of the hybridization of two strands to form a single duplex, I will consider the assembly of progressively more complex structures, including the protein-like folding of a single strand of DNA, DNA origami and DNA bricks. A particular emphasis will be on the complexities that arise from the polymeric and double helical nature of DNA, such as wrapping, threading, and kinetic traps where further assembly progress is topologically inhibited.   

Ion transport across the biological membrane by computational protein design

The cellular membrane is impermeable to most of the chemicals the cell needs to take in or discard to survive. Therefore, transporters---a class of transmembrane proteins tasked with shuttling cargo chemicals in and out of the cell---are essential to all cellular life. From existing crystal structures, we know transporters to be complex machines, exquisitely tuned for specificity and controllability. But how could membrane-bound life have evolved if it needed such complex machines to exist first? To shed light onto this question, we considered the task of designing a transporter de novo. As our guiding principle, we took the ``alternating-access model''---a conceptual mechanism stating that transporters work by rocking between two conformations, each exposing the cargo-binding site to either the intra- or the extra-cellular environment. A computational design framework was developed to encode an anti-parallel four-helix bundle that rocked between two alternative states to orchestrate the movement of Zn(II) ions across the membrane. The ensemble nature of both states was accounted for using a free energy-based approach, and sequences were chosen based on predicted formation of the targeted topology in the membrane and bi-stability. A single sequence was prepared experimentally and shown to function as a Zn(II) transporter in lipid vesicles. Further, transport was specific to Zn(II) ions and several control peptides supported the underlying design principles. This included a mutant designed to retain all properties but with reduced rocking, which showed greatly depressed transport ability. These results suggest that early transporters could have evolved in the context of simple topologies, to be later tuned by evolution for improved properties and controllability. Our study also serves as an important advance in computational protein design, showing the feasibility of designing functional membrane proteins and of tuning conformational landscapes for desired function.