Remote controlled optical manipulation of bimetallic nanoparticle catalysts using peptides
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99 GENERAL AND MISCELLANEOUS↗
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Superconductivity from Luttinger surfaces: Emergent Sachdev-Ye-Kitaev physics with infinite-body interactions
The pairing of two electrons on a Fermi surface due to an infinitesimal attraction between them always results in a superconducting instability at zero temperature (T = 0). The equivalent question of pairing instability on a Luttinger surface (LS)—190a contour of zeros of the propagator—instead leads to a quantum critical point (QCP) that separates a non-Fermi liquid and superconductor. A surprising and little understood aspect of pair fluctuations at this QCP is that their thermodynamics maps to that of the Sachdev-Ye-Kitaev (SYK) model in the strong coupling limit. Here, we offer a simple justification for this mapping by demonstrating that (i) LS models share the reparametrization symmetry of the q → ∞ SYK model with q-body interactions close to the LS, and (ii) the enforcement of gauge invariance results in a $\frac{1}{√τ}$ (τ ~ T -1 ) behavior of the fluctuation propagator near the QCP, as is the feature of SYK conformal Green functions, but leaves the overall form of the free energy map robust.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Data-driven prediction of α IIb β 3 integrin activation paths using manifold learning and deep generative modeling
The integrin heterodimer is a transmembrane protein critical for driving cellular process and is a therapeutic target in the treatment of multiple diseases linked to its malfunction. Activation of integrin involves conformational transitions between bent and extended states. Some of the conformations that are intermediate between bent and extended states of the heterodimer have been experimentally characterized, but the full activation pathways remain unresolved both experimentally due to their transient nature and computationally due to the challenges in simulating rare barrier crossing events in these large molecular systems. An understanding of the activation pathways can provide new fundamental understanding of the biophysical processes associated with the dynamic interconversions between bent and extended states and unveil new putative therapeutic targets. In this work, we apply nonlinear manifold learning to coarse-grained molecular dynamics simulations of bent, extended, and two intermediate states of αI I b β3 integrin to learn a low-dimensional embedding of the configurational phase space. We then train deep generative models to learn an inverse mapping between the low-dimensional embedding and high-dimensional molecular space and use these models to interpolate the molecular configurations constituting the activation pathways between the experimentally characterized states. Furthermore, this work furnishes plausible predictions of integrin activation pathways and reports a generic and transferable multi-scale technique to predict transition pathways for biomolecular systems.
97 MATHEMATICS AND COMPUTING↗
Small angle scattering of diblock copolymers profiled by machine learning
We outline a machine learning strategy for quantitively determining the conformation of AB-type diblock copolymers with excluded volume effects using small angle scattering. Complemented by computer simulations, a correlation matrix connecting conformations of different copolymers according to their scattering features is established on the mathematical framework of a Gaussian process, a multivariate extension of the familiar univariate Gaussian distribution. We show that the relevant conformational characteristics of copolymers can be probabilistically inferred from their coherent scattering cross sections without any restriction imposed by model assumptions. This work not only facilitates the quantitative structural analysis of copolymer solutions but also provides the reliable benchmarking for the related theoretical development of scattering functions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Condensed Constrained Nonconforming Mortar-Based Approach for Preconditioning Finite Element Discretization Problems
This paper presents and studies an approach for constructing auxiliary space preconditioners for finite element problems using a constrained nonconforming reformulation that is based on a proposed modified version of the mortar method. The well-known mortar finite element discretization method is modified to admit a local structure, providing an element-by-element or subdomain-by-subdomain assembly property. This is achieved via the introduction of additional trace finite element spaces and degrees of freedom (unknowns) associated with the interfaces between adjacent elements or subdomains. The resulting nonconforming formulation and a reduced-via-static-condensation Schur complement form on the interfaces are used in the construction of auxiliary space preconditioners for a given conforming finite element discretization problem. Overall, the properties of these preconditioners are studied and their performance is illustrated on model second order scalar elliptic problems utilizing high order elements.
97 MATHEMATICS AND COMPUTING↗
CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps
Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).
59 BASIC BIOLOGICAL SCIENCES↗
Long way to Ricci flatness
We study two-dimensional weighted N = (2) supersymmetric CP models with the goal of exploring their infrared (IR) limit. WCP(N, N ~ ) are simplified versions of world-sheet theories on non-Abelian strings in four-dimensional N = 2 QCD. In the gauged linear sigma model (GLSM) formulation, WCP(N, N ~ ) has N charges +1 and N ~ charges –1 fields. As well-known, at N ~ = N this GLSM is conformal. Its target space is believed to be a non-compact Calabi-Yau manifold. We mostly focus on the N = 2 case, then the Calabi-Yau space is a conifold.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps
Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.
B factors↗
Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations
Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.
59 BASIC BIOLOGICAL SCIENCES↗
Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis
Abstract High‐energy X‐ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long‐range order, but is underutilized for molecular complexes in solution. We demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal⋅⋅⋅metal distances separated by over 12 Å. The metal⋅⋅⋅metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub‐Ångström conformational differences by direct comparison of solution phase and solid‐state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.
Xie, Zhu‐Lin↗
Interacting CFTs for all couplings: thermal versus entanglement entropy at large N
In this paper, I calculate the large N limit of marginal O(N) models with non-polynomial potentials in arbitrary odd dimensions d. This results in a new class of interacting pure conformal field theories (CFTs) in d = 3 + 4n for any n ϵ $\mathbb{Z}$ + . Similarly, in d = 3 + 4n I calculate the thermal entropy for all couplings on R 2+4n × S 1 for n = 0, 1, 2, 3. In 2+1 dimensions I find the strong-to-weak coupling ratio of the thermal entropy to be 4/5, matching recent results, and further extend this analysis to higher odd dimensions. Next, I calculated the vacuum entanglement entropy ${s}_{\textrm{EE}}^d$ on S d–2 for all couplings in arbitrary odd d in the large N limit. I find the vacuum entanglement entropy on S d–2 to be not only solvable but also constant for all couplings λ. Thus, in the large N limit, the vacuum entanglement entropy on S d–2 for odd d is constant for all λ, in contrast to the thermal entropy which is shown to also be monotonically decreasing with λ in d = 3 + 4n.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
A Nonorthogonal Configuration Interaction Approach to Singlet Fission in Perylenediimide Compounds
Perylenediimide molecules constitute a family of chromophores that undergo singlet fission, a process in which an excited singlet state converts into lower energy triplets on two neighboring molecules, potentially increasing the efficiency of organic solar cells. Here, the nonorthogonal configuration interaction method is applied to study the effect of the different crystal packing of various perylenediimide derivatives on the relative energies of the singlet and triplet states, the intermolecular electronic couplings, and the relative rates for singlet fission. The analysis of the wave functions and electronic couplings reveals that charge transfer states play an important role in the singlet fission mechanism. Dimer conformations where the PDI molecules are at large displacements along the long axis and short on the short axis are posed as the most favorable for singlet fission. The role of the substituent at the imide group has been inspected concluding that, although it has no effect in the energies, for some conformations it significantly influences the electronic couplings, and therefore, replacing this substituent with hydrogen may introduce artifacts in the computational modeling of the PDI molecules.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural basis of RNA cap modification by SARS-CoV-2
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5'-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2'-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2'-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.
59 BASIC BIOLOGICAL SCIENCES↗
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (k cat /K M 146 M -1 s -1 ). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (k cat /K M 103,000 M -1 s -1 ) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.
59 BASIC BIOLOGICAL SCIENCES↗
Active conformation of the p97-p47 unfoldase complex
The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a “hand-over-hand” mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.
59 BASIC BIOLOGICAL SCIENCES↗
Elucidation of the physical factors that control activated transport of penetrants in chemically complex glass-forming liquids
Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S 0 ( T ) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S 0 ( T ) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S 0 ( T ) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.
Science & Technology - Other Topics↗
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning
Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.
59 BASIC BIOLOGICAL SCIENCES↗