High-throughput prediction of protein conformational distributions with subsampled AlphaFold2.

This paper presents an innovative approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' ground state conformations and is limited in its ability to predict conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different protein conformations by subsampling multiple sequence alignments. We tested our method against nuclear magnetic resonance experiments on two proteins with drastically different amounts of available sequence data, Abl1 kinase and the granulocyte-macrophage colony-stimulating factor, and predicted changes in their relative state populations with more than 80% accuracy. Our subsampling approach worked best when used to qualitatively predict the effects of mutations or evolution on the conformational landscape and well-populated states of proteins. It thus offers a fast and cost-effective way to predict the relative populations of protein conformations at even single-point mutation resolution, making it a useful tool for pharmacology, analysis of experimental results, and predicting evolution.

Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold 2.

This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' ground state conformations and is limited in its ability to predict conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different protein conformations by subsampling multiple sequence alignments. We tested our method against NMR experiments on two proteins with drastically different amounts of available sequence data, Abl1 kinase and the granulocyte-macrophage colony-stimulating factor, and predicted changes in their relative state populations with more than 80% accuracy. Our subsampling approach worked best when used to qualitatively predict the effects of mutations or evolution on the conformational landscape and well-populated states of proteins. It thus offers a fast and cost-effective way to predict the relative populations of protein conformations at even single-point mutation resolution, making it a useful tool for pharmacology, NMR analysis, and evolution.

Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2.

This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' single ground state conformations and is limited in its ability to predict fold switching and the effects of mutations on conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different conformations of proteins and even accurately predict changes in those populations induced by mutations by subsampling multiple sequence alignments. We tested our method against NMR experiments on two proteins with drastically different amounts of available sequence data, Abl1 kinase and the granulocyte-macrophage colony-stimulating factor, and predicted changes in their relative state populations with accuracies in excess of 80%. Our method offers a fast and cost-effective way to predict protein conformations and their relative populations at even single point mutation resolution, making it a useful tool for pharmacology, analyzing NMR data, and studying the effects of evolution.

Stable recursive auxiliary field quantum Monte Carlo algorithm in the canonical ensemble: Applications to thermometry and the Hubbard model.

Many experimentally accessible, finite-sized interacting quantum systems are most appropriately described by the canonical ensemble of statistical mechanics. Conventional numerical simulation methods either approximate them as being coupled to a particle bath or use projective algorithms which may suffer from nonoptimal scaling with system size or large algorithmic prefactors. In this paper, we introduce a highly stable, recursive auxiliary field quantum Monte Carlo approach that can directly simulate systems in the canonical ensemble. We apply the method to the fermion Hubbard model in one and two spatial dimensions in a regime known to exhibit a significant "sign" problem and find improved performance over existing approaches including rapid convergence to ground-state expectation values. The effects of excitations above the ground state are quantified using an estimator-agnostic approach including studying the temperature dependence of the purity and overlap fidelity of the canonical and grand canonical density matrices. As an important application, we show that thermometry approaches often exploited in ultracold atoms that employ an analysis of the velocity distribution in the grand canonical ensemble may be subject to errors leading to an underestimation of extracted temperatures with respect to the Fermi temperature.

Digital circuits and neural networks based on acid-base chemistry implemented by robotic fluid handling.

Acid-base reactions are ubiquitous, easy to prepare, and execute without sophisticated equipment. Acids and bases are also inherently complementary and naturally map to a universal representation of "0" and "1." Here, we propose how to leverage acids, bases, and their reactions to encode binary information and perform information processing based upon the majority and negation operations. These operations form a functionally complete set that we use to implement more complex computations such as digital circuits and neural networks. We present the building blocks needed to build complete digital circuits using acids and bases for dual-rail encoding data values as complementary pairs, including a set of primitive logic functions that are widely applicable to molecular computation. We demonstrate how to implement neural network classifiers and some classes of digital circuits with acid-base reactions orchestrated by a robotic fluid handling device. We validate the neural network experimentally on a number of images with different formats, resulting in a perfect match to the in-silico classifier. Additionally, the simulation of our acid-base classifier matches the results of the in-silico classifier with approximately 99% similarity.

Machine Learning Diffusion Monte Carlo Forces.

Diffusion Monte Carlo (DMC) is one of the most accurate techniques available for calculating the electronic properties of molecules and materials, yet it often remains a challenge to economically compute forces using this technique. As a result, ab initio molecular dynamics simulations and geometry optimizations that employ Diffusion Monte Carlo forces are often out of reach. One potential approach for accelerating the computation of "DMC forces" is to machine learn these forces from DMC energy calculations. In this work, we employ Behler-Parrinello Neural Networks to learn DMC forces from DMC energy calculations for geometry optimization and molecular dynamics simulations of small molecules. We illustrate the unique challenges that stem from learning forces without explicit force data and from noisy energy data by making rigorous comparisons of potential energy surface, dynamics, and optimization predictions among ab initio density functional theory (DFT) simulations and machine-learning models trained on DFT energies with forces, DFT energies without forces, and DMC energies without forces. We show for three small molecules─C2, H2O, and CH3Cl─that machine-learned DMC dynamics can reproduce average bond lengths and angles within a few percent of known experimental results at one hundredth of the typical cost. Our work describes a much-needed means of performing dynamics simulations on high-accuracy, DMC PESs and for generating DMC-quality molecular geometries given current algorithmic constraints.

Finite-Size Error Cancellation in Diffusion Monte Carlo Calculations of Surface Chemistry.

The accurate prediction of reaction mechanisms in heterogeneous (surface) catalysis is one of the central challenges in computational chemistry. Quantum Monte Carlo methods─Diffusion Monte Carlo (DMC) in particular─are being recognized as higher-accuracy, albeit more computationally expensive, alternatives to Density Functional Theory (DFT) for energy predictions of catalytic systems. A major computational bottleneck in the broader adoption of DMC for catalysis is the need to perform finite-size extrapolations by simulating increasingly large periodic cells (supercells) to eliminate many-body finite-size effects and obtain energies in the thermodynamic limit. Here, we show that it is possible to significantly reduce this computational cost by leveraging the cancellation of many-body finite-size errors that accompanies the evaluation of energy differences when calculating quantities like adsorption (binding) energies and mapping potential energy surfaces. We analyze the cancellation and convergence of many-body finite-size errors in two well-known adsorbate/slab systems, H2O/LiH(001) and CO/Pt(111). Based on this analysis, we identify strategies for obtaining binding energies in the thermodynamic limit that optimally utilize error cancellation to balance accuracy and computational efficiency. Using one such strategy, we then predict the correct order of adsorption site preference on CO/Pt(111), a challenging problem for a wide range of density functionals. Our accurate and inexpensive DMC calculations are found to unambiguously recover the top > bridge > hollow site order, in agreement with experimental observations. We proceed to use this DMC method to map the potential energy surface of CO hopping between Pt(111) adsorption sites. This reveals the existence of an L-shaped top-bridge-hollow diffusion trajectory characterized by energy barriers that provide an additional kinetic justification for experimental observations of CO/Pt(111) adsorption. Overall, this work demonstrates that it is routinely possible to achieve order-of-magnitude speedups and memory savings in DMC calculations by taking advantage of error cancellation in the calculation of energy differences that are ubiquitous in heterogeneous catalysis and surface chemistry more broadly.

Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase.

The rate of modern drug discovery using experimental screening methods still lags behind the rate at which pathogens mutate, underscoring the need for fast and accurate predictive simulations of protein evolution. Multidrug-resistant bacteria evade our defenses by expressing a series of proteins, the most famous of which is the 29-kilodalton enzyme, TEM ß-lactamase. Considering these challenges, we applied a covalent docking heuristic to measure the effects of all possible alanine 237 substitutions in TEM due to this codon's importance for catalysis and effects on the binding affinities of commercially-available ß-lactam compounds. In addition to the usual mutations that reduce substrate binding due to steric hindrance, we identified two distinctive specificity-shifting TEM mutations, Ala237Arg and Ala237Lys, and their respective modes of action. Notably, we discovered and verified through minimum inhibitory concentration assays that, while these mutations and their bulkier side chains lead to steric clashes that curtail ampicillin binding, these same groups foster salt bridges with the negatively-charged side-chain of the cephalosporin cefixime, widely used in the clinic to treat multi-resistant bacterial infections. To measure the stability of these unexpected interactions, we used molecular dynamics simulations and found the binding modes to be stable despite the application of biasing forces. Finally, we found that both TEM mutants also bind strongly to other drugs containing negatively-charged R-groups, such as carumonam and ceftibuten. As with cefixime, this increased binding affinity stems from a salt bridge between the compounds' negative moieties and the positively-charged side chain of the arginine or lysine, suggesting a shared mechanism. In addition to reaffirming the power of using simulations as molecular microscopes, our results can guide the rational design of next-generation ß-lactam antibiotics and bring the community closer to retaking the lead against the recurrent threat of multidrug-resistant pathogens.

LYRUS: a machine learning model for predicting the pathogenicity of missense variants.

SUMMARY: Single amino acid variations (SAVs) are a primary contributor to variations in the human genome. Identifying pathogenic SAVs can provide insights to the genetic architecture of complex diseases. Most approaches for predicting the functional effects or pathogenicity of SAVs rely on either sequence or structural information. This study presents 〈Lai Yang Rubenstein Uzun Sarkar〉 (LYRUS), a machine learning method that uses an XGBoost classifier to predict the pathogenicity of SAVs. LYRUS incorporates five sequence-based, six structure-based and four dynamics-based features. Uniquely, LYRUS includes a newly proposed sequence co-evolution feature called the variation number. LYRUS was trained using a dataset that contains 4363 protein structures corresponding to 22 639 SAVs from the ClinVar database, and tested using the VariBench testing dataset. Performance analysis showed that LYRUS achieved comparable performance to current variant effect predictors. LYRUS's performance was also benchmarked against six Deep Mutational Scanning datasets for PTEN and TP53. AVAILABILITY AND IMPLEMENTATION: LYRUS is freely available and the source code can be found at https://github.com/jiaying2508/LYRUS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.

Real-time dynamics of strongly correlated fermions using auxiliary field quantum Monte Carlo.

Spurred by recent technological advances, there is a growing demand for computational methods that can accurately predict the dynamics of correlated electrons. Such methods can provide much-needed theoretical insights into the electron dynamics probed via time-resolved spectroscopy experiments and observed in non-equilibrium ultracold atom experiments. In this article, we develop and benchmark a numerically exact Auxiliary Field Quantum Monte Carlo (AFQMC) method for modeling the dynamics of correlated electrons in real time. AFQMC has become a powerful method for predicting the ground state and finite temperature properties of strongly correlated systems mostly by employing constraints to control the sign problem. Our initial goal in this work is to determine how well AFQMC generalizes to real-time electron dynamics problems without constraints. By modeling the repulsive Hubbard model on different lattices and with differing initial electronic configurations, we show that real-time AFQMC is capable of accurately capturing long-lived electronic coherences beyond the reach of mean field techniques. While the times to which we can meaningfully model decrease with increasing correlation strength and system size as a result of the exponential growth of the dynamical phase problem, we show that our technique can model the short-time behavior of strongly correlated systems to very high accuracy. Crucially, we find that importance sampling, combined with a novel adaptive active space sampling technique, can substantially lengthen the times to which we can simulate. These results establish real-time AFQMC as a viable technique for modeling the dynamics of correlated electron systems and serve as a basis for future sampling advances that will further mitigate the dynamical phase problem.

Secret messaging with endogenous chemistry.

Data encoded in molecules offers opportunities for secret messaging and extreme information density. Here, we explore how the same chemical and physical dimensions used to encode molecular information can expose molecular messages to detection and manipulation. To address these vulnerabilities, we write data using an object's pre-existing surface chemistry in ways that are indistinguishable from the original substrate. While it is simple to embed chemical information onto common objects (covers) using routine steganographic permutation, chemically embedded covers are found to be resistant to detection by sophisticated analytical tools. Using Turbo codes for efficient digital error correction, we demonstrate recovery of secret keys hidden in the pre-existing chemistry of American one dollar bills. These demonstrations highlight ways to improve security in other molecular domains, and show how the chemical fingerprints of common objects can be harnessed for data storage and communication.

Leveraging autocatalytic reactions for chemical domain image classification.

Autocatalysis is fundamental to many biological processes, and kinetic models of autocatalytic reactions have mathematical forms similar to activation functions used in artificial neural networks. Inspired by these similarities, we use an autocatalytic reaction, the copper-catalyzed azide-alkyne cycloaddition, to perform digital image recognition tasks. Images are encoded in the concentration of a catalyst across an array of liquid samples, and the classification is performed with a sequence of automated fluid transfers. The outputs of the operations are monitored using UV-vis spectroscopy. The growing interest in molecular information storage suggests that methods for computing in chemistry will become increasingly important for querying and manipulating molecular memory.

Finite temperature auxiliary field quantum Monte Carlo in the canonical ensemble.

Finite temperature auxiliary field-based quantum Monte Carlo methods, including determinant quantum Monte Carlo and Auxiliary Field Quantum Monte Carlo (AFQMC), have historically assumed pivotal roles in the investigation of the finite temperature phase diagrams of a wide variety of multidimensional lattice models and materials. Despite their utility, however, these techniques are typically formulated in the grand canonical ensemble, which makes them difficult to apply to condensates such as superfluids and difficult to benchmark against alternative methods that are formulated in the canonical ensemble. Working in the grand canonical ensemble is furthermore accompanied by the increased overhead associated with having to determine the chemical potentials that produce desired fillings. Given this backdrop, in this work, we present a new recursive approach for performing AFQMC simulations in the canonical ensemble that does not require knowledge of chemical potentials. To derive this approach, we exploit the convenient fact that AFQMC solves the many-body problem by decoupling many-body propagators into integrals over one-body problems to which non-interacting theories can be applied. We benchmark the accuracy of our technique on illustrative Bose and Fermi-Hubbard models and demonstrate that it can converge more quickly to the ground state than grand canonical AFQMC simulations. We believe that our novel use of HS-transformed operators to implement algorithms originally derived for non-interacting systems will motivate the development of a variety of other methods and anticipate that our technique will enable direct performance comparisons against other many-body approaches formulated in the canonical ensemble.

Observation of a Symmetry-Forbidden Excited Quadrupole-Bound State.

We report the observation of a symmetry-forbidden excited quadrupole-bound state (QBS) in the tetracyanobenzene anion (TCNB-) using both photoelectron and photodetachment spectroscopies of cryogenically-cooled anions. The electron affinity of TCNB is accurately measured as 2.4695 eV. Photodetachment spectroscopy of TCNB- reveals selected symmetry-allowed vibronic transitions to the QBS, but the ground vibrational state was not observed because the transition from the ground state of TCNB- (Au symmetry) to the QBS (Ag symmetry) is triply forbidden by the electric and magnetic dipoles and the electric quadrupole. The binding energy of the QBS is found to be 0.2206 eV, which is unusually large due to strong correlation and polarization effects. A centrifugal barrier is observed for near-threshold autodetachment, as well as relaxations from the QBS vibronic levels to the ground and a valence excited state of TCNB-. The current study shows a rare example where symmetry selection rules, rather than the Franck-Condon principle, govern vibronic transitions to a nonvalence state in an anion.

Polarization of Valence Orbitals by the Intramolecular Electric Field from a Diffuse Dipole-Bound Electron.

The diffuse electron in a dipole-bound state is spatially well separated from the valence electrons and is known to have negligible effects on the dipole-bound state's molecular structure. Here, we show that a dipole-bound state is observed in deprotonated 4-(2-phenylethynyl)-phenoxide anions, 348 cm-1 below the anion's detachment threshold. The photodetachment of the dipole-bound electron is observed to accompany a simultaneous shakeup process in valence orbitals in this aromatic molecular anion. This shakeup process is due to configuration mixing as a result of valence orbital polarization by the intramolecular electric field of the dipole-bound electron. This observation suggests that dipole-bound anions can serve as a new platform to probe how oriented electric fields influence the valence electronic structure of polyatomic molecules.

Observation of a π-Type Dipole-Bound State in Molecular Anions.

We report the observation of a π-type dipole-bound state (π-DBS) in cryogenically cooled deprotonated 9-anthrol molecular anions (9AT^{-}) by resonant two-photon photoelectron imaging. A DBS is observed 191 cm^{-1} (0.0237 eV) below the detachment threshold, and the existence of the π-DBS is revealed by a distinct (s+d)-wave photoelectron angular distribution. The π-DBS is stabilized by the large anisotropic in-plane polarizability of 9AT. The population of the dipole-forbidden π-DBS is proposed to be via a nonadiabatic coupling with the dipole-allowed σ-type DBS mediated by molecular rotations.

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness.

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism's fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 ß-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of ß-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon ß-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 ß-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in ß-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of ß-lactamase's fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

Principles of Information Storage in Small-Molecule Mixtures.

Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of smaller non-polymeric molecules to preserve, process, and transmit information. In this paper, we present a general framework for quantifying chemical memory, which is not limited to polymers and extends to mixtures of molecules of all types. We show that the theoretical limit for molecular information is two orders of magnitude denser by mass than DNA, although this comes with different practical constraints on total capacity. We experimentally demonstrate kilobyte-scale information storage in mixtures of small synthetic molecules, and we consider some of the new perspectives that will be necessary to harness the information capacity available from the vast non-genomic chemical space.

Multicomponent molecular memory.

Multicomponent reactions enable the synthesis of large molecular libraries from relatively few inputs. This scalability has led to the broad adoption of these reactions by the pharmaceutical industry. Here, we employ the four-component Ugi reaction to demonstrate that multicomponent reactions can provide a basis for large-scale molecular data storage. Using this combinatorial chemistry we encode more than 1.8 million bits of art historical images, including a Cubist drawing by Picasso. Digital data is written using robotically synthesized libraries of Ugi products, and the files are read back using mass spectrometry. We combine sparse mixture mapping with supervised learning to achieve bit error rates as low as 0.11% for single reads, without library purification. In addition to improved scaling of non-biological molecular data storage, these demonstrations offer an information-centric perspective on the high-throughput synthesis and screening of small-molecule libraries.