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1. Surveying biomolecular frustration at atomic resolution

   https://doi.org/10.1038/s41467-020-19560-9  

   Chen, Mingchen; Chen, Xun; Schafer, Nicholas P.; Clementi, Cecilia; Komives, Elizabeth A.; Ferreiro, Diego U.; Wolynes, Peter G. (December 2020, Nature Communications)

   null (Ed.)

   Abstract To function, biomolecules require sufficient specificity of interaction as well as stability to live in the cell while still being able to move. Thermodynamic stability of only a limited number of specific structures is important so as to prevent promiscuous interactions. The individual interactions in proteins, therefore, have evolved collectively to give funneled minimally frustrated landscapes but some strategic parts of biomolecular sequences located at specific sites in the structure have been selected to be frustrated in order to allow both motion and interaction with partners. We describe a framework efficiently to quantify and localize biomolecular frustration at atomic resolution by examining the statistics of the energy changes that occur when the local environment of a site is changed. The location of patches of highly frustrated interactions correlates with key biological locations needed for physiological function. At atomic resolution, it becomes possible to extend frustration analysis to protein-ligand complexes. At this resolution one sees that drug specificity is correlated with there being a minimally frustrated binding pocket leading to a funneled binding landscape. Atomistic frustration analysis provides a route for screening for more specific compounds for drug discovery. 

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2. Building blocks of non-Euclidean ribbons: size-controlled self-assembly via discrete frustrated particles

   https://doi.org/10.1039/D2SM01371A  

   Hall, Douglas M.; Stevens, Mark J.; Grason, Gregory M. (February 2023, Soft Matter)

   Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current challenge is to understand the connection between microscopic physical properties of misfitting “building blocks” and emergent assembly behavior at the mesoscale. We present and analyze a particle-based description of what is arguably the best studied example for frustrated soft matter assembly, negative-curvature ribbon assembly, observed in both assemblies of chiral surfactants and shape-frustrated nanoparticles. Based on our particle model, known as saddle wedge monomers, we numerically test the connection between microscopic shape and interactions of the misfitting subunits and the emergent behavior at the supra-particle scale, specifically focussing on the propagation and relaxation of inter-particle strains, the emergent role of extrinsic shape on frustrated ribbons and the equilibrium regime of finite width selection. Beyond the intuitive role of shape misfit, we show that self-limitation is critically dependent on the finite range of cohesive interactions, with larger size finite assemblies requiring increasing short-range interparticle forces. Additionally, we demonstrate that non-linearities arising from discrete particle interactions alter self-limiting behavior due to both strain-softening in shape-flattened assembly and partial yielding of highly strained bonds, which in turn may give rise to states of hierarchical, multidomain assembly. Tracing the regimes of frustration-limited assembly to the specific microscopic features of misfitting particle shapes and interactions provides necessary guidance for translating the theory of size-programmable assembly into design of intentionally-frustrated colloidal particles. 

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3. Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families

   https://doi.org/10.1093/nar/gkae244  

   Parra, R Gonzalo; Freiberger, Maria I; Poley-Gil, Miriam; Fernandez-Martin, Miguel; Radusky, Leandro G; Ruiz-Serra, Victoria; Wolynes, Peter G; Ferreiro, Diego U; Valencia, Alfonso (April 2024, Nucleic Acids Research)

   Abstract According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families. 

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4. Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations

   https://doi.org/https://doi.org/10.1021/acs.macromol.2c00141  

   Erin Tsai, Hishara Keshani (June 2022, Macromolecules)

   Electrostatic interactions play a significant role in regulating biological systems and have received increasing attention due to their usefulness in designing advanced stimulus-responsive materials. Polypeptoids are highly tunable N-substituted peptidomimetic polymers that lack backbone hydrogen bonding and chirality. Therefore, polypeptoids are suitable systems to study the effect of noncovalent interactions of substituents without complications of backbone intramolecular and intermolecular hydrogen bonding. In this study, all-atom molecular dynamics (MD) simulations were performed on micelles formed by a series of sequence-defined ionic polypeptoid block copolymers consisting of a hydrophobic segment and a hydrophilic segment in an aqueous solution. By combining the results from MD simulations and experimental small-angle neutron scattering data, further insights were gained into the internal structure of the formed polypeptoid micelles, which is not always directly accessible from experiments. In addition, information was gained into the physics of the noncovalent interactions responsible for the self-assembly of weakly charged polypeptoids in an aqueous solution. While the aggregation number is governed by electrostatic repulsion of the negatively charged carboxylate (COO–) substituents on the polypeptoid chain within the micelle, MD simulations indicate that the position of the charge on singly charged chains mediates the shape of the micelle through the charge–dipole interactions between the COO– substituent and the surrounding water. Therefore, the polypeptoid micelles formed from the single-charged series offer the possibility for tailorable micelle shapes. In contrast, the polypeptoid micelles formed from the triple-charged series are characterized by more pronounced electrostatic repulsion that competes with more significant charge–sodium interactions, making it difficult to predict the shape of the micelles. This work has helped further develop design principles for the shape and structure of self-assembled micelles by controlling the position of charged moieties on the backbone of polypeptoid block copolymers. 

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5. Dispersed, Condensed, and Self-Limiting States of Geometrically Frustrated Assembly

   https://doi.org/10.1103/PhysRevX.13.041010  

   Hackney, Nicholas W.; Amey, Christopher; Grason, Gregory M. (October 2023, Physical Review X)

   In self-assembling systems, geometric frustration leads to complex states characterized by internal gradients of shape misfit. Frustrated assemblies have drawn recent interest due to the unique possibility that their thermodynamics can sense and select the finite size of assembly at length scales much larger than constituent building blocks or their interactions. At present, self-limitation is chiefly understood to derive from zero-temperature considerations, specifically the competition between cohesion and scale-dependent elastic costs of frustration. While effects of entropy and finite-temperature fluctuations are necessarily significant for self-assembling systems, their impact on the self-limiting states of frustrated assemblies is not known. We introduce a generic, minimal model of frustrated assembly and establish its finite-temperature and concentration-dependent thermodynamics by way of simulation and continuum theory. The phase diagram is marked by three distinct states of translation order: a dispersed vapor, a defect-riddled condensate, and the self-limiting aggregate state. We show that, at finite temperature, the self-limiting state is stable at intermediate frustration. Furthermore, in contrast to the prevailing picture, its thermodynamic boundaries with the macroscopic disperse and bulk states are temperature controlled, pointing to the essential importance of translational and conformational entropy in their formation. 

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