An important question is how well the models submitted to CASP retain the properties of target structures. We investigate several properties related to binding. First we explore the binding of small molecules as probes, and count the number of interactions between each residue and such probes, resulting in a binding fingerprint. The similarity between two fingerprints, one for the X‐ray structure and the other for a model, is determined by calculating their correlation coefficient. The fingerprint similarity weakly correlates with global measures of accuracy, and GDT_TS higher than 80 is a necessary but not sufficient condition for the conservation of surface binding properties. The advantage of this approach is that it can be carried out without information on potential ligands and their binding sites. The latter information was available for a few targets, and we explored whether the CASP14 models can be used to predict binding sites and to dock small ligands. Finally, we tested the ability of models to reproduce protein–protein interactions by docking both the X‐ray structures and the models to their interaction partners in complexes. The analysis showed that in CASP14 the quality of individual domain models is approaching that offered by X‐ray crystallography, and hence such models can be successfully used for the identification of binding and regulatory sites, as well as for assembling obligatory protein–protein complexes. Success of ligand docking, however, often depends on fine details of the binding interface, and thus may require accounting for conformational changes by simulation methods.
Protein‐protein interactions are critical to protein function, but three‐dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting for molecular motions to optimize rigid 3D translations and rotations. However, such approaches can be computationally expensive, and faster, less accurate approximations may prove useful for large‐scale prediction and assembly of 3D structures of multi‐protein complexes. We asked if a reduced representation of protein geometry retains enough information about molecular properties to predict pairwise protein interaction interfaces that are tolerant of limited structural rearrangements. Here, we describe a reduced representation of 3D protein accessible surfaces on which molecular properties such as charge, hydrophobicity, and evolutionary rate can be easily mapped, implemented in the MorphProt package. Pairs of surfaces are compared to rapidly assess partner‐specific potential surface complementarity. On two available benchmarks of 185 overall known protein complexes, we observe predictions comparable to other structure‐based tools at correctly identifying protein interaction surfaces. Furthermore, we examined the effect of molecular motion through normal mode simulation on a benchmark receptor‐ligand pair and observed no marked loss of predictive accuracy for distortions of up to 6 Å Cα‐RMSD. Thus, a shape reduction of protein surfaces retains considerable information about surface complementarity, offers enhanced speed of comparison relative to more complex geometric representations, and exhibits tolerance to conformational changes.
more » « less- NSF-PAR ID:
- 10381971
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Proteins: Structure, Function, and Bioinformatics
- Volume:
- 89
- Issue:
- 3
- ISSN:
- 0887-3585
- Page Range / eLocation ID:
- p. 348-360
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Summary We combined optical and atomic force microscopy to observe morphology and kinetics of microstructures (typically referred to as bees) that formed at free surfaces of unmodified Performance Graded (PG) 64‐22 asphalt binders upon cooling from 150°C to room temperature (RT) at 5°C min–1, and changes in these microstructures when the surface was terminated with a transparent solid (glass) or liquid (glycerol) overlayer. The main findings are: (1) at free binder surfaces, wrinkled microstructures started to form near the crystallization temperature (∼45°C) of saturates such as wax observed by differential scanning calorimetry, then grew to ∼5 µm diameter, ∼25 nm wrinkle amplitude and 10–30% surface area coverage upon cooling to RT, where they persisted indefinitely without observable change in shape or density. (2) Glycerol coverage of the binder surface during cooling reduced wrinkled area and wrinkle amplitude three‐fold compared to free binder surfaces upon initial cooling to RT; continued glycerol coverage at RT eliminated most surface microstructures within ∼4 h. (3) No surface microstructures were observed to form at binder surfaces covered with glass. (4) Submicron bulk microstructures were observed by near‐infrared microscopy beneath the surfaces of all binder samples, with size, shape and density independent of surface coverage. No tendency of such structures to float to the top or sink to the bottom of mm‐thick samples was observed. (5) We attribute the dependence of surface wrinkling on surface coverage to variation in interface tension, based on a thin‐film continuum mechanics model.
Lay Description Asphalt binder, or bitumen, is the glue that holds aggregate particles together to form a road surface. It is derived from the heavy residue that remains after distilling gasoline, diesel and other lighter products out of crude oil. Nevertheless, bitumen varies widely in composition and mechanical properties. To avoid expensive road failures, bitumen must be processed after distillation so that its mechanical properties satisfy diverse climate and load requirements. International standards now guide these mechanical properties, but yield varying long‐term performance as local source composition and preparation methods vary.
In situ diagnostic methods that can predict bitumen performance independently of processing history are therefore needed. The present work focuses on one promising diagnostic candidate: microscopic observation of internal bitumen structure. Past bitumen microscopy has revealed microstructures of widely varying composition, size, shape and density. A challenge is distinguishing bulk microstructures, which directly influence a binder's mechanical properties, from surface microstructures, which often dominate optical microscopy because of bitumen's opacity and scanning‐probe microscopy because of its inherent surface specificity. In previously published work, we used infrared microscopy to enhance visibility of bulk microstructure. Here, as a foil to this work, we use visible‐wavelength microscopy together with atomic‐force microscopy (AFM) specifically to isolatesurface microstructure, to understand its distinct origin and morphology, and to demonstrate its unique sensitivity to surface alterations. To this end, optical microscopy complements AFM by enabling us to observe surface microstructures form at temperatures (50°C–70°C) at which bitumen's fluidity prevents AFM, and to observe surface microstructure beneath transparent, but chemically inert, liquid (glycerol) and solid (glass) overlayers, which alter surface tension compared to free surfaces. From this study, we learned, first, that, as bitumen cools, distinctly wrinkled surface microstructures form at the same temperature at which independent calorimetric studies showed crystallization in bitumen, causing it to release latent heat of crystallization. This shows that surface microstructures are likely precipitates of the crystallizable component(s). Second, a glycerol overlayer on the cooling bitumen results in smaller, less wrinkled, sparser microstructures, whereas a glass overlayer suppresses them altogether. In contrast, underlying smaller bulk microstructures are unaffected. This shows that surface tension is the driving force behind formation and wrinkling of surface precipitates. Taken together, the work advances our ability to diagnose bitumen samples noninvasively by clearly distinguishing surface from bulk microstructure. -
Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein–protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.more » « less
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null (Ed.)Adsorption of biomolecules onto material surfaces involves a potentially complex mechanism where molecular species interact to varying degrees with a heterogeneous material surface. Surface adsorption studies by atomic force microscopy, sum frequency generation spectroscopy, and solid-state NMR detect the structures and interactions of biomolecular species that are bound to material surfaces, which, in the absence of a solid–liquid interface, do not exchange rapidly between surface-bound forms and free molecular species in bulk solution. Solution NMR has the potential to complement these techniques by detecting and studying transiently bound biomolecules at the liquid–solid interface. Herein, we show that dark-state exchange saturation transfer (DEST) NMR experiments on gel-stabilized TiO2 nanoparticle (NP) samples detect several forms of biomolecular adsorption onto titanium(IV) oxide surfaces. Specifically, we use the DEST approach to study the interaction of amino acids arginine (Arg), lysine (Lys), leucine (Leu), alanine (Ala), and aspartic acid (Asp) with TiO2 rutile NP surfaces. Whereas Leu, Ala, and Asp display only a single weakly interacting form in the presence of TiO2 NPs, Arg and Lys displayed at least two distinct bound forms: a species that is surface bound and retains a degree of reorientational motion and a second more tightly bound form characterized by broadened DEST profiles upon the addition of TiO2 NPs. Molecular dynamics simulations indicate different surface bound states for both Lys and Arg depending on the degree of TiO2 surface hydroxylation but only a single bound state for Asp regardless of the degree of surface hydroxylation, in agreement with results obtained from the analysis of DEST profiles.more » « less
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Abstract Increasing numbers of protein interactions have been identified in high-throughput experiments, but only a small proportion have solved structures. Recently, sequence coevolution-based approaches have led to a breakthrough in predicting monomer protein structures and protein interaction interfaces. Here, we address the challenges of large-scale interaction prediction at residue resolution with a fast alignment concatenation method and a probabilistic score for the interaction of residues. Importantly, this method (EVcomplex2) is able to assess the likelihood of a protein interaction, as we show here applied to large-scale experimental datasets where the pairwise interactions are unknown. We predict 504 interactions de novo in the
E. coli membrane proteome, including 243 that are newly discovered. While EVcomplex2 does not require available structures, coevolving residue pairs can be used to produce structural models of protein interactions, as done here for membrane complexes including the Flagellar Hook-Filament Junction and the Tol/Pal complex.
