Excluded volume entropic effects on protein unfolding times and intermediary stability

Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof

Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.

RNA-assisted self-assembly of monomeric antigens into virus-like particles as a recombinant vaccine platform

Representing highly ordered repetitive structures of antigen macromolecular assemblies, virus-like particles (VLPs) serve as a high-priority vaccine platform against emerging viral infections, as alternatives to traditional cell culture-based vaccines. RNAs can function as chaperones (Chaperna) and are extremely effective in promoting protein folding. Beyond their canonical function as translational adaptors, tRNAs may moonlight as chaperones for the kinetic control of macromolecular antigen assembly. Capitalizing on genomic RNA co-assembly in infectious virions, we present the first report of a biomimetic assembly of viral capsids that was assisted by non-viral host RNAs into genome-free, non-infectious empty particles. Here, we demonstrate the assembly of bacterially-produced soluble norovirus VP1 forming VLPs (n = 180) in vitro. A tRNA-interacting domain (tRID) was genetically fused with the VP1 capsid protein, as a tRNA docking tag, in the bacterial host to transduce chaperna function for de novo viral antigen folding. tRID/tRNA removal prompted the in vitro assembly of monomeric antigens into highly ordered repetitive structures that elicited robust protective immune responses after immunization. The chaperna-based assembly of monomeric antigens will impact the development and deployment of VLP vaccines for emerging and re-emerging viral infections.

Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation

The dynamics of protein folding are complicated because of the various types of amino acid interactions that create secondary, supersecondary, and tertiary interactions. Computational modeling can be used to simulate the biophysical and biochemical interactions that determine protein folding. Effective folding to a desired protein configuration requires a compromise between speed, stability, and specificity. If the primary sequence of amino acids emphasizes one of these characteristics, the others might suffer and the folding process may not be optimized. We provide an example of a model peptide whose primary sequence produces a highly stable supersecondary two-helix bundle structure, but at the expense of lower speed and specificity of the folding process. We show how computational simulations can be used to discover the configuration of the kinetic trap that causes the degradation in the speed and specificity of folding. We also show how amino acid sequences can be engineered by specific substitutions to optimize the folding to the desired supersecondary structure.

Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories

Thermodynamic parameters such as free energies and heat capacities are important quantities for understanding processes involving structural transitions in complex molecules such as proteins. Computational investigations provide simulated data that can be used for calculating thermodynamic parameters. However, calculations give accurate results only if the simulations sample all of configuration space with the appropriate temperature-dependent Boltzmann equilibrium probabilities. For many systems, truly comprehensive sampling of configuration space is not computationally feasible. We present an approximation technique for the calculations that will give accurate values for thermodynamic parameters when the data is incomplete. Our work is applicable to systems in which there are two distinct, important regions of configuration space that must be sampled. Importantly, the results are also valid when the system is more complex than two-state systems. Transition pathways that involve intermediate configurations between two stable regions are allowed in this treatment, and therefore the results are valid for multistate systems.

Statistical thermodynamics of liquid-liquid phase separation in ternary systems during complex coacervation

Liquid-liquid phase separation leading to complex coacervation in a ternary system (oppositely charged polyion and macroion in a solvent) is discussed within the framework of a statistical thermodynamics model. The polyion and the macroion in the ternary system interact to form soluble aggregates (complexes) in the solvent, which undergoes liquid-liquid phase separation. Four necessary conditions are shown to drive the phase separation: (i) (σ{23}){3}r/Φ{23c}≥(64/9α{2})(χ{23}Φ{3}){2} , (ii) r≥[64(χ{23}Φ{3}){2}/9α{2}σ{23}{3}]{1/2}, (iii) χ{23}≥(2χ{231}-1)/Φ{23c}Φ{3}, and (iv) (σ{23}){2}/sqrt[I]≥8/3α(2χ{231}-1) (where σ{23} is the surface charge on the complex formed due to binding of the polyelectrolyte and macroion, Φ{23c} is the critical volume fraction of the complex, χ{23} is the Flory interaction parameter between polyelectrolyte and macroion, χ{231} is the same between solvent and the complex, Φ{3} is the volume fraction of the macroions, I is the ionic strength of the solution, α is electrostatic interaction parameter and r is typically of the order of molecular weight of the polyions). It has been shown that coacervation always requires a hydrated medium. In the case of a colloidal macroion and polyelectrolyte coacervation, molecular weight of polyelectrolyte must satisfy the condition r≥10{3} Da to exhibit liquid-liquid phase separation. This model has been successfully applied to study the coacervation phenomenon observed in aqueous Laponite (macroion)-gelatin (polyion) system where it was found that the coacervate volume fraction, δΦ{23}∼χ{231}{2} (where δΦ{23} is the volume fraction of coacervates formed during phase separation). The free energy and entropy of this process have been evaluated, and a free-energy landscape has been drawn for this system that maps the pathway leading to phase separation.

Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide

Protein folding times are many orders of magnitude shorter than would occur if the peptide chain randomly sampled possible configurations, which implies that protein folding is a directed process. The detailed shape of protein's energy landscape determines the rate and reliability of folding to the native state, but the large number of structural degrees of freedom generates an energy landscape that is hard to visualize because of its high dimensionality. A commonly used picture is that of an energy funnel leading from high energy random coil state down to the low energy native state. As lattice computer models of protein dynamics become more realistic, the number of possible configurations becomes too large to count directly. Statistical mechanic and thermodynamic approaches allow us to count states in an approximate manner to quantify the entropy and energy of the energy landscape within a folding funnel for an alpha-helical protein. We also discuss the problems that arise in attempting to count the huge number of individual states of the random coil at the top of the funnel.

Free-energy landscape of alcohol driven coacervation transition in aqueous gelatin solutions

Liquid-liquid phase separation of a homogeneous polyampholyte (gelatin) solution into a dense polymer-rich coacervate and the dilute supernatant phase is discussed through free-energy landscape formalism. We have evaluated the free energy and entropy of the system as it undergoes the phenomenon of simple coacervation, driven by the addition of a nonsolvent. Electrophoretic mobility (mu) and turbidity measurements were performed on 0.01% and 0.05% (w/v) aqueous gelatin solutions that were driven towards coacervation by the addition of ethanol. The mobility of the polyampholyte molecules, which was typically mu approximately 0.38+/-0.02 microm/s cm/V in water, gradually reduced for the soluble intermolecular complexes to a plateau value of mu approximately 0.11+/-0.01 microm/s cm/V as the ethanol volume fraction equaled phi(ns) approximately 0.47+/-0.03, which coincided with the first appearance of coacervate droplets (coacervation transition) observed from turbidity measurements, a behavior found to be invariant of gelatin concentration. These results were used as input to the theoretical model to explicitly construct the free-energy landscape for a single gelatin chain and the global system comprising the polymer-rich coacervate and the dilute supernatant phase.

Self-organization in protein folding and the hydrophobic interaction

Self-organization is a critical aspect of living systems. During the folding of protein molecules, the hydrophobic interaction plays an important role in the collapse of the peptide chain to a compact shape. As the hydrophobic core tightens and excludes water, not only does the number of hydrophobic side chain contacts increase, but stabilization is further enhanced by an increase in strength of each hydrophobic interaction between side chains in the core. Thus, the self-organization of the protein folding process augments itself by enhancing the stability of the core against large-scale motions that would unfold the protein. Through calculations and computer simulations on a model four-helix bundle protein, we show how the strengthening of the hydrophobic interaction is crucial for stabilizing the core long enough for completion of the folding process and quantitatively manifests self-organizing dynamical behavior.

Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model α-helical hairpin peptide

The presence of non-native kinetic traps in the free energy landscape of a protein may significantly lengthen the overall folding time so that the folding process becomes unreliable. We use a computational model alpha-helical hairpin peptide to calculate structural free energy landscapes and relate them to the kinetics of folding. We show how protein engineering through strategic changes in only a few amino acid residues along the primary sequence can greatly increase the speed and reliability of the folding process, as seen experimentally. These strategic substitutions also prevent the formation of long-lived misfolded configurations that can cause unwanted aggregations of peptides. These results support arguments that removal of kinetic traps, obligatory or nonobligatory, is crucial for fast folding.