Inferring protein 3D structure from deep mutation scans

Abstract

We describe an experimental method of three-dimensional (3D) structure determination that exploits the increasing ease of high-throughput mutational scans. Inspired by the success of using natural, evolutionary sequence co-variation to compute protein and RNA folds, we explored whether ‘laboratory’, synthetic sequence variation might also yield 3D structures. We analyzed five large-scale mutational scans and discovered that the pairs of residues with the largest positive epistasis in the experiments are sufficient to determine the 3D fold. We show that the strongest epistatic pairings from genetic screens of three proteins, a ribozyme, and a protein interaction reveal 3D contacts within and between macromolecules. Using these experimental epistatic pairs, we compute ab initio folds for a GB1 domain (within 1.8 Å of the crystal structure) and a WW domain (2.1 Å). We propose strategies that reduce the number of mutants needed for contact prediction, suggesting that genomics-based techniques can efficiently predict 3D structure.

Introduction

Amino acid pairs in a protein are considered epistatic when the combined effect of mutating both residues is different than would be expected from the individual mutations if they had independent effects. Epistatic interactions have been observed between nearby residues in structure, suggesting that it may be possible to determine the 3D fold of a protein from phenotype assays if direct contacts dominate the strongest epistasis. In this case, targeted genetics experiments that leverage the increasing ability to assay thousands of mutated sequences for functional effects, might be sufficient to determine a protein’s 3D fold (Fig. 1). Analogously, evolutionary coupling methods have used natural sequence variation to predict 3D structures, suggesting that ‘laboratory’, synthetic sequence variation might also yield accurate 3D structures. If genetic screens can provide enough structural information to predict the fold of a protein or RNA molecule, the increasing ease of mutant library generation and sequencing could be used to accelerate protein and RNA structure determination.

Fig. 1. Genetic experiments can be used to discover epistatic interactions and solve 3D fold.

Mutant genes can be assayed (top) to reveal functional and structural interactions (middle). It is possible to create and test libraries sufficient enough to determine 3D structure (bottom).

The success of computational approaches, such as evolutionary couplings, depends on large alignments of natural sequences to predict 3D structures ab initio by identifying pairs of residues likely to be in contact ^1–8. These computational methods, although powerful, are limited by the availability of large and diverse sequence families from the natural environment. Building the requisite alignments can be particularly challenging for mammalian-specific protein complexes and disordered regions. Even when considering individual protein domains such as those in the PFAM database ⁹, roughly 70% of the domains of unknown structure have insufficient sequences for use in evolutionary covariation methods (unpublished data, models available at evcouplings.org). Extracting structural information from laboratory-created sequence variants could help solve the structure of some of these proteins.

In recent years, technological advances in sequencing have enabled high-throughput investigation of the effects of tens to hundreds of thousands of mutations in parallel (sometimes called “deep mutational scanning”, or DMS studies) ^10–38, opening the door to more systematic explorations. In these high-throughput genetic experiments, a large library of mutant sequences is synthesized, followed by selection for some phenotype of transformed cells or of the protein or RNA products, e.g. ligand binding or structural stability ³³. By sequencing the library before and after selection, the fitness of each mutant can be defined according to the change in corresponding sequence counts after selection. Therefore, high-throughput mutational scans can provide fitness measurements of thousands of sequence variants for a protein, where fitness is measured with respect to a particular phenotype.

However, being able to infer structure blindly from double mutation experiments relies critically on epistasis evidencing residues in direct contact. Studies have shown that epistasis can occur between residues that are spatially close in 3D structure ^39–43, and experimentally determined epistatic pairs have even been used to discriminate incorrect decoys from correct structures generated from homology models ^44,45. Nevertheless, other studies have reported that strong epistasis between distant residues may reflect allostery or functional binding sites ^38,46,47. However, most studies have measured a low proportion of all mutant pairs, and therefore the relationship between epistasis and contacting residues has not been quantified systematically nor used to predict ab initio 3D folds.

Here we test whether contacts can be predicted directly from epistasis data, by computing the epistasis at pairs of positions from high-throughput mutational scans on the GB1 domain of protein G in Streptococcus sp. group G ⁴², the WW domain of the human Yap1 ¹⁸, the second RRM domain of S. cerevisiae Pab1 ¹³, the helical interaction in the Fos and Jun heterodimer ⁴³, and the Twister ribozyme of O. sativa ³⁶. For each study, we find that the strongest instances of positive epistasis reveal 3D contacts in the corresponding molecule. For the assays that measured pairs throughout most of the sequence – namely, the GB1 and WW proteins - we find the predicted contacts are sufficient to blindly determine the native 3D folds. Similarly, for Fos and Jun, the contacts predicted by epistasis are sufficient to determine the arrangement of the heterodimer complex. We also demonstrate that designed mutant libraries with fewer mutants can be used to determine 3D contacts and to fold structures to similar accuracy as the full set of possible doubles. Our results together indicate that high-throughput mutational scans coupled to functional assays can provide a method of determining protein and RNA structures.

Results

Epistasis reveals positions in 3D contact

To investigate whether epistasis can be used to blindly identify 3D contacts, we assembled five high-throughput mutational scan datasets that extensively measure double mutations. The scans of the GB1 domain ⁴², Fos-Jun dimer ⁴³, and Twister ribozyme ³⁶ include nearly all double mutations, whereas those of the WW domain ¹⁸ and the RRM domain ¹³ are much sparser (Supplementary Fig. 1, Supplementary Table 1). For each dataset, we computed the epistasis of all measured double mutants where the single mutants are also measured, using the epistasis model best correlated with measured fitness (Supplementary Fig. 2, Supplementary Table 1). A multiplicative model provided the best projection for every assay except that of Fos-Jun, which was better fit by a thermodynamic model ⁴³.

Based on the idea that direct interactions in 3D might exhibit the strongest epistasis, we tested whether the most epistatic residue-residue pairs were proximal in known structures of each molecule. We identified the most epistatic pairs by sorting all pairs of positions by the corresponding double mutant with the strongest positive epistasis (Supplementary Fig. 3, Supplementary Table 2). To evaluate 3D contact precision, we measure the fraction of the top L/2 and L pairs within 5 Å in experimental structures (L = sequence length), according to a convention in structure prediction that arose due to folded proteins having a number of contacts proportional to sequence length ^2,6,8,48 (Methods, Supplementary Table 3). Precision of the top positive epistatic pairs compared to true 3D contacts are reported for all five macromolecules. Similarly, we found the pairs with the largest negative and largest magnitude epistasis to often be proximal in 3D, but far less consistently than those with largest positive epistasis (Supplementary Table 3).

GB1 domain:

Olson et al. ⁴² assayed all single and almost all pairwise mutations of the 56 amino acid GB1 domain of Streptococcal protein G, including 535,917 out of 555,940 possible double amino acid mutations, for binding to human immunoglobulin G (IgG). While the experiment is very comprehensive, an experimental measurement floor interferes with the calculation of epistasis for at least 30% of double mutants. We then ranked all amino acid pairs by the maximum positive epistasis measured in corresponding double mutants, and found 68% of the top L/2 long-range pairs to be within 5Å in any of the 3D structures of GB1 ^49–57. The probability of randomly drawing pairs with at least that many contacts is 1.26 × 10⁻¹³, by the hypergeometric test (Methods, Fig. 2a, Table 1, Supplementary Table 3). As weaker epistatic pairs are included, the precision with respect to proximity drops dramatically (Supplementary Fig. 4, Supplementary Table 3), suggesting why previous studies that are sparse or use a much lower threshold for epistasis would not have revealed a strong signal for structure ⁴².

Fig. 2. Experimental epistasis pairs reveal structural contacts in GB1 protein.

a. Maximum value of positive epistasis for each possible pair of residues in the GB1 domain, analyzed from Olson et al. (42) (Supplementary Tables 1 and 2). The most positive epistatic pairs (dark blue) suggest tertiary contacts. b. The 38 top positive epistatic pairs (black) include 28 (L/2) long-range (|i-j| > 5) pairs and 10 local pairs (L: length of protein, Supplementary Table 2). These pairs are used to fold the protein and to determine the topological arrangement of secondary structure elements (orange arrows). Epistatic pairs (black) are overlaid on the true contacting pairs in the NMR structure 2gb1 (48) (minimum heavy atom distance between two residues; dark blue, 5 Å cutoff; light blue, 8 Å cutoff). c. Secondary structure, from top to bottom: observed secondary structure from 2gb1 (48); β strand scores from epistasis values; α helical scores (Methods and Supplementary Table 4); and average per position and full single experimental mutation effect matrices showing concordance with local epistasis scores. d. Epistasis pairs (black) plotted on the 3D structure 2gb1.

Table 1. Percentage of correctly predicted contacts (true positives) using various forms of epistasis.

The percent of predicted contacts according to residues with any heavy atom within 5 Å over multiple experimentally determined structures for GB1 (PDBs listed in Supplementary Table 3). Precisions are shown for the largest positive, negative, or absolute measured epistasis with differing numbers of top-ranked pairs (including both long-range and local pairs).

	top 20 pairs	top 30 pairs	top 40 pairs	top 50 pairs	top 100 pairs
Positive epistasis	90%	80%	78%	68%	61%
Negative epistasis	25%	27%	30%	38%	32%
Absolute epistasis	40%	40%	40%	44%	38%

The ‘local’ epistatic pairs (those separated by 5 or fewer residues in sequence) also provide useful information about secondary structure, as was seen in work on evolutionary couplings ⁵. We scored residues according to the maximum positive epistasis measured at corresponding pairs expected to be close in an α-helix or a β-strand, and the resultant propensities largely overlap with the known secondary structure of GB1 (α-helix P value = 6.84 × 10⁻⁵, β-strand P value = 1.03 × 10⁻⁴ by t test) (Fig. 1b, Supplementary Table 4, Supplementary Fig. 5). Specifically, there are four peaks in β-strand propensity, roughly corresponding to the correct secondary structure, and one large peak in α propensity in the same location as the true helix (Fig. 2b). There are also two small α-helical signals (Supplementary Fig. 5) that are inconsistent with the second and third β-strands, which could be noise or, more speculatively, could reflect known GB1 fold-switching ^58–60.

Because the strongest positive epistatic pairs of GB1 were enriched in true residue-residue contacts, we were encouraged to infer a 3D model from the pairs (Results).

WW domain:

Araya et al. tested 47,000 variants of the 37 amino acid human Yap1 WW domain for binding to a peptide ligand ¹⁸. Only 4% (8,797/ 202,521) of all possible double mutations can be tested for epistasis, and this level of sparsity may explain why the precision of the top L/2 long-range is much lower than for GB1 (39%, P value = 1.60 × 10⁻²). The sparsity of data also limited our ability to score secondary structure propensity (Supplementary Fig. 5). Nevertheless, many of the false positives (7/11) are still closer than 8 Å, and the predicted contacts reveal the correct overall fold topology ^61–65 (Fig. 3a).

Fig. 3. Experimental epistasis pairs reveal contacts in WW domain, RRM domain, and Twister Ribozyme.

a. WW. The top 22 positive epistatic pairs (black) include 18 (L/2) long-range pairs and are close in 3D (dark blue, 5 Å cutoff; light blue, 8 Å cutoff) in the WW domain of human Yap1, analyzed from Araya et al. (18) (Supplementary Tables 1 and 2). b. RRM. Residue pairs that display strong positive epistasis in the second RRM domain in yeast Pab1, analyzed from Melamed et al. (13) (Supplementary Tables 1 and 2). The experiment measured effects of all pairs only within blocks of 25 residues in linear sequence (Fragments 1, 2, and 3) and not between them. Therefore, experimental epistasis data exist only for the shaded square regions on the contact map. The top 38 (L/2) positive epistatic pairs (black) are close in the observed 3D structure 1cvj (65) (dark blue, 5 Å cutoff; light blue, 8 Å cutoff). c. Twister. Left: Contact map showing the 35 nucleotide pairs with the strongest positive epistasis (black), including 24 (L/2) long-range pairs (|i-j| > 5), compared to true contacts from the crystal structure 4oji (70) (dark blue, 5 Å cutoff; light blue, 8 Å cutoff). Strongly epistatic pairs are measured at the pseudoknot contacts (gray circles), and multiple nucleotides – both proximal and non-proximal in 4oji – share strong epistasis with the cleaved nucleotide A7 (dashed gray circle). Right: Two nonstandard pairs (in green: 46A and 28A, left insert; 25C and 7A, right insert) are high-scoring epistatic pairs when compared to 4oji (RNA structure, blue; magnesium ions, yellow).

RRM domain:

Melamed et al. assayed 110,745 variants of the second RRM domain of Pab1 (75 amino acids). Mutations were confined to three 25 amino acid fragments, such that double mutants occur within an individual fragment, but not between fragments. Of the doubles measured, 36,522 could be evaluated for epistasis (3.6% of the 1,001,775 possible across the length of RRM, 11.2% of the 324,900 possible within the three fragments mutated) ¹³. Because the measurements are confined to fragments, we can only predict contacts between relatively local sequence positions (positions i and j, such that |i – j| ≤ 25) (Fig. 3b, Supplementary Fig. 1) and therefore include local pairs in the following reported precisions. The top L/2 (37) epistatic pairs have a precision of 54% < 5 Å contacts (P value = 7.72 × 10⁻⁴) ^66,67. Though the mutation scan does not sample long-range pairs essential to determine the fold of the full protein, we do observe epistatic pairs consistent with the β-hairpins in fragments 2 and 3 (Fig. 3b).

Fos-Jun heterodimer:

Diss and Lehner performed a high-throughput mutational scan of the 32-residue regions that heterodimerize between the bZip proteins, Fos and Jun, when binding DNA ⁴³. These data allow us to test whether epistasis measurements can also reveal the interfaces and arrangement of protein complexes. The top L/2 (16) epistatic pairs between Fos and Jun have a contact precision of 50% < 5 Å (distance < 5 Å, P value = 8.78 × 10⁻⁸) (Supplementary Fig. 4 and 6). In general, far fewer than L/2 contacts are sufficient to determine the arrangement of a protein complex ^3,68. The top seven epistatic pairs are sufficient to reveal the parallel interface and helix-helix register, with five of these residue pairs within 5 Å in the experimental structure 1fos ⁶⁹ (Supplementary Fig. 6).

Twister ribozyme:

The twister ribozyme, a noncoding RNA molecule that self-cleaves, adopts a pseudoknot tertiary structure important for its catalytic activity ^70,71. Kobori and Yokobayashi performed a high-throughput mutational scan of the O. sativa Osa-1–4 twister ribozyme, assaying all possible single and double mutants of the 48-nucleotide cleaved section ³⁶. Each variant was assayed for the fraction of copies cleaved, which we interpret as fitness, allowing us to compute epistasis for all pairs of positions. Positive epistasis was again the most informative in identifying proximal nucleotides; 50% of the top long-range L/2 epistatic pairs of residues are within 5 Å (P value = 2.01 × 10⁻⁸), including multiple pseudoknot contacts ^71,72 (Fig. 3c, left). Two of the top three most positive epistatic pairs, C26-G48 and 14C–30G, correspond to the two long-range interactions that define the tertiary fold of this ribozyme forming a pseudoknot ⁷¹. The top L/2 epistatic pairs also include interactions that are neither Watson-Crick nor wobble base pairings. For example, the trans non-Watson-Crick pairing A28-A46 is strongly epistatic and is thought to help position the active site nucleotide A7 in the structure, in addition to forming part of a pseudoknot (Fig. 3c, right) ⁷¹. The A7-C25 pair (also in our top L/2 positive epistatic pairs) connects the active site nucleotide and the magnesium ion coordinating C25. Pseudoknot pairs, non-Watson-Crick pairs, and metal-mediated interactions can be critical for 3D structure computation but are typically absent or poorly predicted by RNA secondary structure methods ⁷³. Since these high-throughput mutational scans can reveal these essential tertiary interactions, they could be an efficient method for 3D RNA structure determination.

Strong epistatic pairs not in contact are often part of functional sites

The non-contacting epistatic pairs in each molecule tended to involve residues at the binding or active sites (Supplementary Fig. 7). In GB1, all nine of the false positives in the top L/2 pairs are clustered at the binding surface with IgG, around residues A250 and G267. In WW, the majority (nine out of eleven) of non-contacting epistatic pairs are clustered around Y188, N191, or T197 at the ligand interface. In RRM, eight of eighteen false positives are clustered around S155 and V198. Finally, in Twister six of the twelve false positives include the cleaved nucleotide A7. Although these epistatic pairs likely reflect functional relationships between distal residues, they can confound how we use epistasis measurements to predict folding. Assays for experimental phenotypes that more directly measure stability of the 3D fold may result in fewer false positives in predicted contacts by our method.

3D folds can be determined from epistasis

We tested whether the pairs of positions with high positive epistasis are sufficient to fold the protein ab initio, i.e. from an extended polypeptide chain. By analogy to folding methods using evolutionary couplings ^1,2,48, we applied constraints on up to L pairs of positions (L = sequence length) to generate several hundred models using the distance geometry and simulated annealing protocol in the Crystallography and NMR System package (CNS) ⁷⁴. Using a variable number of constraints allows us to test a wider variety of folds by applying different sets of distance restraints. Top models are then selected from all of the generated models by a blind ranking score (Methods).

GB1 folding:

We folded GB1 from a fully extended polypeptide using the epistatic pairs as distance constraints, along with hydrogen bond constraints from predicted β-sheet topology and registrations. We ranked models blindly by how well they satisfied the input constraints (Methods, Supplementary Fig. 8). Of the 25 top-ranked candidates, the best structure is 1.8 Å C-α rmsd over 49 residues to the nearest experimental structure (2.2 Å C-α to all 56 in 2gb1). Even folding without hydrogen bond constraints, the best model in the 25 top-ranked is 2.5 C-α rmsd over 49 residues (3.3 C-α to all 56 in 2gb1) ⁴⁹ (Fig. 4a, Supplementary Table 5).

Fig. 4. Predicted 3D structures from experimental epistasis scores alone.

a. GB1 (gray) generated from positive epistatic pairs, compared to the NMR structure 2gb1 (48) (blue). The predicted structure is within 1.8 Å C-α rmsd of the known structure over 49/56 residues. b. WW domain generated from positive epistatic pairs, compared to the NMR structure 1jmq (61) (blue). Models and structures are represented with secondary structure cartoons (left) and backbone ribbons (right).

WW folding:

We folded WW using the same procedure as GB1. Due to significant variation between experimental structures of WW (0.9–3.4 Å C-α rmsd), we restricted our comparison to the 22-residue region we found to be consistent across structures (177–198, 0.6–2.7 Å C-α rmsd) (Supplementary Table 6). The best model in the 25 top-ranked is 2.1 Å C-α rmsd over that full region in the closest structure 1jmq ⁶² (Fig. 4b, Supplementary Table 5, Supplementary Fig. 8).

Fos-Jun docking:

We docked idealized monomers using constraints on residues from the 7 highest epistasis resulting in 3D heterodimers with C-$\alpha$ rmsd of 0.99 Å over 58 residues (1.5 Å over 64 residues to 1fos) ⁶⁹. This result is much more accurate than a model docked without those constraints, 5.4 Å over 58 residues (Supplementary Fig. 6).

In general, we found that folding with epistatic pair constraints results in more accurate structure prediction than by ab initio protocols alone; blind folding with Rosetta ⁷⁵ achieves 4.0 Å C-$\alpha$ rmsd for GB1 and 3.8 Å for WW (Supplementary Fig. 9).

3D folds can be determined from much smaller mutant libraries

Generalizing this mutational scanning approach to large proteins would be infeasible if all possible double mutations needed to be assayed; for instance, testing a 300-residue length protein would mean synthesizing and assaying 16 million sequences (scaling with L²). We therefore considered whether partial libraries of fewer mutants could be used to solve 3D folds reliably. We tested three strategies of sampling just a fraction of all double mutants: (i) unguided sampling of any double mutations at random, (ii) partially guided sampling of doubles including a detrimental single mutant, and (iii) pairwise guided sampling of detrimental single mutant pairs. Experimentally, these strategies can be implemented using error-prone PCR (i,ii) or doped oligonucleotide synthesis (i,ii,iii). We tested each strategy in silico at various library sizes by sampling subsets of the full GB1 dataset, evaluating the precision of predicted contacts and accuracy of 3D folds (n = 1,000 and n = 10 random draws, respectively) (Fig. 5, Supplementary Table 7). For equivalent library sizes, the guided strategies had consistently higher 3D contact precision, raising both the lower bound and the median of sampling outcomes (Fig. 5a). Comparable folding accuracy to that of the full dataset (2.2 Å all residue C-$\alpha$ rmsd) was achieved reliably for mutant libraries 50%, 25%, and 5% the size of the full library for the three respective experimental strategies (Fig. 5b).

Fig. 5. Only a small fraction of all double mutants is needed to determine 3D fold.

a. The precision of L/2 long-range epistatic pairs in contact (minimum heavy atom distance within 5 Å) is plotted for various fractional samples (n = 1,000 each) of the full double mutant library, sampled according to three strategies: completely unguided mutations (gray), pairs of one or more deleterious single mutations (pink), and pairs of two deleterious mutations (red). Precision comparable to that of the full GB1 double mutant dataset (dashed line) is consistently achieved using just 50%, 25%, and 5% as many mutants, for each respective strategy. Central lines in all box-and-whiskers plots correspond to the median, box boundaries represent the first and third quartiles, and whiskers show the range excluding suspected outliers (> Quartile 3 + 1.5 × interquartile range or < Quartile 1 – 1.5 × interquartile range). b. For each of these experimental strategies and library sizes, we folded from the epistatic pairs computed from 10 different random samples and here plot the C-α rmsd of the final predictions. Notably, the third strategy consistently achieved folds more accurate than that of the full dataset (dashed line). Box-and-whisker plots are defined as above. c. 3D ensembles of the final folding results for each 5% subsample versus 2gb1 (48) (blue) illustrate how guided mutations can improve both the accuracy and consistency of models predicted from epistasis measured in small datasets.

In summary, using guided filtering informed by single-mutation experiments reduces the search space of structurally meaningful epistatic pairs, suggesting that it may be possible to compute the structure of larger proteins with a fraction of the effort of all-pair scans.

Discussion

This work shows that the pairs of sequence positions with strongest positive epistasis are overwhelmingly close in 3D and can be systematically identified by mutation scans with sufficient coverage to determine protein folds. In order to generalize the use of genetic experiments for structure determination, several computational and experimental challenges must be addressed.

Computationally, we need better methods of inferring true contacts from phenotypic measurements, and of computing folds from those contacts. For instance: (i) False positives could arise as the result of an insufficiently accurate model of epistasis and be reduced by models that account for non-linear effects of independent mutations, correcting for systematic biases (Supplementary Fig. 2). (ii) Some true epistatic pairs may be distant in 3D structure (e.g. through transitive interactions) and may be removed as predicted contacts using methods that have been applied to evolutionary couplings to deconvolve these types of indirect interactions ^6,76,77. (iii) Folding biomolecules accurately from predicted contacts can be a challenge when there are false positives, and will benefit from recent advances in structure determination that iteratively discard non-satisfied constraints ^78–80. Meanwhile, folding RNA from base couplings is still a particular challenge even with extra 3D information ^81,82.

Regarding the genetic experiments, the challenges are the availability of assays and the ability to cover sufficient sequence diversity. (i) Mutational scans require a phenotypic assay that can be coupled one-to-one to sequences with appropriate dynamic range and functional mapping. The assays considered here make use of phenotypes specific to the studied molecule, and could be difficult to generalize to an arbitrary gene. Nevertheless, newer methods promise to address this problem, e.g., by coupling GFP to a target protein to assay for cellular abundance and thermostability ⁸³. (ii). Despite the falling costs of sequencing and synthesis, strategies of creating smaller libraries for measuring epistasis may be required to extend structure prediction to larger proteins, RNAs, and complexes. We show here that simple experimental strategies can reduce the number of sequences necessary by at least an order of magnitude, and more sophisticated strategies could reduce the number even further.

In summary, these results highlight how small, laboratory-scale sequence diversity coupled to quantitative assays is sufficient to determine 3D structures of proteins and RNA, in contrast to the large amount of evolutionary sequence diversity previously used for structure prediction ^2,68. An independent effort by J. Schmiedel and B. Lehner ⁸⁴ also yields high-quality 3D structures of the GB1 domain based on analysis of epistasis patterns in the Olson et al. mutation scan⁴², suggesting that the results are robust to different approaches. Given that 3D structure could be determined with unguided libraries, we anticipate far broader applications with the use of designed libraries, for example the 3D determination of large biomolecules and complexes.

Methods

Calculation of epistasis from experimental data

We calculate epistasis ($ϵ$) using the multiplicative model, defined as the log ratio between double mutant fitness or activity values (W_ab) and the product of constituent single mutant fitnesses (W_a and W_b):

$$\epsilon =ln{W}_{ab}-{\left(ln{W}_a+ln{W}_b\right)}_{capped}$$

Therefore, epistasis is defined as the signed deviation of observed fitness from fitness as projected by $ln{W}_a+ln{W}_b$. Where this projection exceeds the maximum or minimum fitness measured in an assay, we fix it to the maximum or minimum fitness value: ${\left(ln{W}_a+ln{W}_b\right)}_{capped}$. Additional information can be found in the Life Sciences Reporting Summary.

GB1 domain:

Olson et al. synthesized 99.97% of all double mutants (535,917/536,085) and all single mutants (1,045) in the first GB domain of protein G (GB1) by randomly combining variants of 11 5-residue cassettes, created by saturation mutagenesis ⁴². Fitness of each individual mutant was defined as the ratio of sequence reads before and after selection of mutant proteins by IgG binding, normalized by the ratio observed for the wild type. The pre-selection input counts of double mutants vary between 1–64,627. As lower input counts sensitize measurements to noise, we excluded all mutants with fewer than 20 pre-selection read counts from analysis. This filtering step removes ~3% of the synthesized double mutants. Since non-specific adsorption onto IgG beads led to a fitness of approximately 0.01, all experimental or projected fitness values smaller than this were set to 0.01. This measurement floor makes negative epistasis particularly hard to measure, as > 30% of double mutants may have been more deleterious than measured in the assay.

WW domain:

Araya et al. generated 47,000 mutants in the 34-residue WW domain of the hYAP65 protein by chemical assembly using a mixture of wild-type and mutant oligonucleotides ^18,85. 4.4% of all possible double mutants (8,870/202,521) were synthesized that also had corresponding single mutants in the library. These proteins were presented by bacteriophage and selected by binding to a target peptide fixed to magnetic beads. Araya et al. found fitness as the slope of the log ratio of counts before and after selection (‘enrichment’) over three rounds of selection, corrected for non-specific selection and normalized against the slope for the wild type.

RRM domain:

Melamed et al. created three separate mutation libraries for 25-residue regions of the second RRM domain of the essential yeast gene Pab1, expressed the mutants in BY4741 yeast, and selected under doxycycline until log phase. Fitness was found as the ratio of initial sequence reads to those after selection ¹³. For this protein, we use the epistasis values calculated by the authors, who also use a multiplicative model and measured epistasis for 12.2% of possible double mutants within the pairwise sites mutated (39,608/334,900).

Fos-Jun heterodimer:

Diss and Lehner created all single mutations (608 each) in 32 amino acid regions of both the Fos and Jun leucine zipper domains by overlap-extension PCR, then cloned random pairings of Fos and Jun mutants into plasmids by Gibson assembly to obtain 29% of all trans Fos-Jun double mutants (107,625/369,664) ⁴³. In their experiment, Fos and Jun are fused to separate fragments of DHFR, which confers yeast with resistance to methotrexate when the regions are complexed together. Yeast transformed with these mutant combinations were sequenced before and after competition under methotrexate selection. Diss and Lehner compute a protein-protein interaction score as the log₂ ratio of relative optical density (OD x read fraction) after selection versus before selection, normalizing by that of the wild type. They remove background growth by subtracting the mean score of stop mutants. Diss and Lehner computed epistasis by the multiplicative model as well as a fitted thermodynamic model, which they show to better describe the fitness of double mutants for this assay. We use the epistasis values computed for the thermodynamic fit, preferred by the authors.

Twister ribozyme:

Kobori and Yokobashi synthesized all double (10,296) and all single (144) mutants of the Osa 1–4 ribozyme, excluding the 6nt region that is removed by self-cleavage ³⁶. A pool of RNA mutants was synthesized from a mutant-doped oligonucleotide mixture in vitro, given time to self-cleave, and then sequenced. The resultant sequence reads record counts of cleaved and un-cleaved mutants. Relative activity of a mutant was defined as the fraction of reads found cleaved for that variant, normalized by the fraction cleaved for the wild type.

Estimating secondary structure from patterns in epistasis

Epistasis between local residues was used to score the propensity of individual positions towards the α-helix or β-strand conformations. This score was developed by Toth-Petroczy et al. to predicts α and β propensities from local evolutionary couplings ⁵ corresponding to the spatial patterns in β-strands (i+1 distant, i+2 proximal) and α−helices (i+1, i+2 distant, i+3, i+4 proximal):

$${\beta }_{score,i}=\frac{\left(A_{i+2}-A_{i+1}\right)}{St{d}_{i+1}}$$

$${\alpha }_{score,i}=\frac{\left(A_{i+3}+A_{i+4}-A_{i+1}-A_{i+2}\right)}{St{d}_{i+1}}$$

Here $A_{i+n}$ is the maximum positive epistasis averaged at (i, i+n) and (i, i-n), and normalized by the correlation between values at i+1 and i+n determined by Toth-Petroczy et al. across 3,800 protein families for evolutionary couplings ⁵ (values in Supplementary Table 4, code available at <https://github.com/debbiemarkslab/3D_from_DMS_Extended_Data>). Scores are shown both for individual positions, and when smoothed by averaging the β score across i to i+1 and the α score across i to i+3 (Supplementary Fig. 5).

Predicting β−sheet contacts from epistasis

We predicted which β-strand pairs were hydrogen bond partners according to which pairs of strands had the largest epistasis value for a residue-residue pair between the two strands. At maximum, each β-strand was partnered with two other strands, and strands were only paired together if they were in each other’s top two hits. To account for potential β−hairpins, we assumed that strands with a linker of ≤ 5 residues were partners and had an antiparallel orientation. These simple rules were sufficient to predict the correct sheet topology for the GB1 and WW mutational scans.

The register between partner strands was selected as the strand alignment that places the largest epistatic pair in contact and that maximizes the number of strand-strand hydrogen bonds (or in other words, maximizes the total overlap of the two strands). If the orientation (antiparallel vs. parallel) was not identified by the length of the linker region connecting the two partnered strands, we used the highest and second-highest epistatic pair between the two strands to determine whether antiparallel or parallel strand bonding was more consistent with the two residue-residue pairs. Two possible patterns of hydrogen bonding based on this register were then separately applied to folding as distance restraints (3 ± 0.5 Å) between corresponding nitrogen and oxygen atoms in the protein backbone. Full code is provided at <https://github.com/debbiemarkslab/3D_from_DMS_Extended_Data>.

Folding from epistasis contacts

We generated 3D folds of the GB1 domain starting from an extended polypeptide by applying distance restraints between the top long-range (> 5 amino acids apart) epistatic pairs. These constraints were input to the distance geometry and simulated annealing protocols in the Crystallography and NMR System (CNS) package as follows: (i) distance restraints (2–4 Å) between the most distal heavy atoms of sidechains specified by the top epistatic pairs, (ii) angle and distance restraints specified by secondary structure, and (iii) when indicated, predicted β-sheet contacts as described above ^1,2 (CNS input files at <https://github.com/debbiemarkslab/3D_from_DMS_Extended_Data>). Secondary structure specifications for GB1 were based on predictions from the PSIPRED 4.0 webserver ^86,87. The β-strand scores were ambiguous in some regions, and therefore we ran three corresponding secondary structure ranges (β1: 228–235, β2: 238/239/240–246, β3: 268–272, and β4: 276–282) and ranked all models together in one group. We computed 10 models folded using the top-scoring 10, 11, …, ascending up to 56 (L) epistatic constraints using the previously described protocol ⁶, and blindly ranked these models (Methods, below). WW was folded according to the same method, using up to 36 (L) pairwise constraints, with the secondary structure ranges scored by PSIPRED (β1: 177–181, β2: 187–191, and β3: 196–199).

Ranking – Blindly identifying the top ab initio model

We ranked each ab initio model by how well it satisfies the constraints used for folding. We calculate the equal-weighted sum of the extent to which: the top L epistatic pairs are contacting as described in ^48,68, the predicted hydrogen bond partners are contacting, and the backbone angles meet the constraints set by predicted secondary structure according to a method described in ² (Supplementary Fig. 8, scoring code in <https://github.com/debbiemarkslab/3D_from_DMS_Extended_Data>).

$$score=\frac{contactscore+hbondscore+2^{o}score}{3}$$

The contact score is computed according to the weighted sigmoid function described in Kamisetty et al. to blindly score models based on the proximity of residue-residue pairs predicted to be in contact (46):

$$contactscore=\sum _{n=1}^L{w}_n*sigmoid\left(C\beta dis{t}_n,\eta ,\kappa \right)$$

$C\beta dis{t}_n$ is the $C_{\beta }$-$C_{\beta }$ distance between residues in pair n. The parameters $\eta$ and $\kappa$ determine the activation distance and steepness of the sigmoid for a given amino acid pair, and are given by Kamisetty et al. (46). We also used epistasis to infer β-sheet hydrogen bonds, which we scored analogously to the epistasis pairs, but chose sigmoid parameters to describe the distance between partner residues in a β-sheet:

$$hbondscore=\sum _{n=1}^{L}sigmoid\left(C\alpha dis{t}_n,6\text{Å},2\text{Å}\right)$$

Lastly, we measure how well dihedral angles within predicted α-helix and β-strand regions of each model agree with typical α-helix or β-strand angles by the method described in Marks et al. ². This code is part of the EVcouplings software package, available at: https://github.com/debbiemarkslab/EVcouplings.

Docking Fos-Jun from epistatic contacts

We built two idealized helices, each 32 residues long, in PyMol and used these as the input monomer files to the Haddock2.2 webserver ⁸⁸. Monomer residues corresponding to Fos were numbered from 1–32, and residues for Jun were numbered from 33–64. Default settings for docking were used, besides specifying 7 unambiguous restraints corresponding to the 7 most positive epistatic pairs of residues. Each distance restraint was set to a distance of 2.0, with a possible range specified of 2.0 + 0 or −2.0. For the null model, we specified all residues to be active site residues but without any unambiguous distance restraints. All other settings were kept as default. For each run, we took the top-ranked model as supplied by Haddock and compared to the crystal structure of the heterodimer, PDB 1fos ⁶⁹.

Sampling, finding precision, and folding of smaller mutation scans

To determine how precisely 3D contacts can be estimated from mutation scans of smaller libraries, we generated 1,000 independent random samples from the full GB1 dataset, measuring the precision of L/2 (28) and L (56) long-range epistatic pairs. We also tested how precisely 3D fold can be solved from these predicted contacts, but were restricted to 10 samples for each library size and strategy due to the computational cost of folding. The sampling code is provided at <https://github.com/debbiemarkslab/3D_from_DMS_Extended_Data>, and resulting precisions can be found in Supplementary Table 7. Folding was performed as described above in Methods. For the guided library approaches, we define deleterious mutations as those in the lower fitness quartile (261/1,045) of single mutants. 43% of measured double mutants (229,421/536,085) include at least one deleterious mutant, and 13% (68,251/536,085) are pairs of deleterious mutants.

Ab initio folding with Rosetta

We benchmarked the precision of our folding results against that of folds determined without predicted contacts, via Rosetta ab initio folding. The Rosetta protocol works by assembling 10,000 models from short 3-mer and 9-mer fragments of experimental structures, and then scoring each according to approximate physical interactions and common bond angles observed in proteins ⁸⁹. We therefore generated 10,000 models for the GB1 and WW sequences, scored them with Rosetta, and compared the structures to the native crystal structures.

Statistical tests

The hypergeometric distribution was used to compute the probability of obtaining, out of all pairs, at least the number of true contacts (< 5 Å) observed in the epistatic pairs for each mutational scan, with results reported in the text as P values. Enrichment of secondary structure elements was computed using the one-tailed Student’s t test for two independent samples, positions outside versus within secondary structure regions (degrees of freedom = # of scored positions – 2. For α and β respectively, GB1 = 45 and 49, WW = 24 and 28, RRM = 49 and 61).