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.
- Award ID(s):
- 2107685
- PAR ID:
- 10511671
- Publisher / Repository:
- Journal of the American Chemical Society
- Date Published:
- Journal Name:
- Journal of the American Chemical Society
- Volume:
- 145
- Issue:
- 50
- ISSN:
- 0002-7863
- Page Range / eLocation ID:
- 27672 to 27679
- Subject(s) / Keyword(s):
- Foldamers, frustration, frustrated interactions, switchable, non-covalent interactions, stimulus responsive
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Abstract -
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.more » « less
-
Abstract Dynamically cross‐linked polymer networks have attracted significant interest in recent years due to their unique and improved properties including increased toughness, malleability, shape memory, and self‐healing. Here, a computational study on the mechanical behavior of dynamically cross‐linked polymer networks is presented. Coarse grained models for different polymer network configurations are established and their mechanical properties using molecular dynamics (MD) simulations are predicted. Consistent with the experimental measurements, the simulation results show that interpenetrating networks (IPN) withstand considerably higher stress compared to the single networks (SN). Additionally, the MD results demonstrate that the origin of this variation in mechanical behavior of IPN and SN configurations goes back to the difference in spatial degrees of freedom of the noncovalent cross‐linkers, represented by nonbonded interactions within the two system types. The results of this work provide new insight for future studies on the design of systems with dual dynamic cross‐linkers where one linkage exchanges rapidly and provides autonomic dynamic character, while the other is a stimulus responsive dynamic covalent linkage that provides stability with dynamic exchange on‐demand.
-
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.
-
Abstract Despite recent advances in polyelectrolyte systems, designing responsive hydrogel interfaces to meet application requirements still proves challenging. Here, semicrystalline colloidal gels composed of poly(methacrylamide‐co‐methacrylic acid) are investigated in water with storage moduli in the MPa range. A combination of SEM, X‐ray scattering, and NMR reveals the evolution of the colloidal microstructure, crystallinity, and hydrogen bonding with varying monomer ratio. The gels with the finest colloidal microstructure exhibit the most dissipative rheological behavior and are selected for the study of their interfacial characteristics and underlying interactions. Microstructure stabilization and dynamics results from short‐range (attractive) hydrogen bonding and hydrophobic forces, and long‐range (repulsive) electrostatic interactions—the “SALR” pair potential. Further, the gel's surface exhibits a submicron colloidal topography that greatly determines (colloidal‐like) friction as a result of the viscoelastic deformation of the colloidal network, while electrostatic near‐surface interactions propagate in lamellar adhesion. The dynamic and reversible nature of the involved interactions introduces a stimulus responsive behavior that enables the electrotunability of adhesion and friction. This study advances the knowledge necessary to design complex hydrogel interfaces that enable spatial and dynamic control of surface properties, which is of relevance for applications in biomedical devices, soft tissue design, soft robotics, and other engineered tribosystems.