Cited by 2Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

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WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families

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Abstract

Water structure is crucially important to protein function and catalysis and can be conserved throughout related proteins despite differences in sequence. The complex hydrogen-bonding networks formed by water molecules and protein residues have been studied extensively, and graph-theory-based methods have frequently been used to describe these networks. Although there exist a number of tools which can be used to track water positions and networks, corresponding methods for easily analyzing complex water network structure across related proteins are limited. To address this challenge, we present here a new tool, WatCon, an open-source Python package which can be used to analyze water positions and water network structure across protein families using both dynamic and static structural information. Importantly, WatCon can be used to classify conservation of water networks, characterize water networks across structures, and project subsequent results for easy visual interpretation. To illustrate WatCon usage, we provide five example applications illustrating WatCon analyses of static structures, dynamic trajectories, and cross-family analysis. This in turn showcases the utility of WatCon for enhancing our understanding of biochemical systems, predicting water hotspots of potential relevance to protein engineering and predicting pathogenic mutations. WatCon can be downloaded at https://github.com/kamerlinlab/WatCon and is available under the GNU General Public License v3.0.

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Figures

1 Schematic overview of the WatCon Python package. Note that analysis can be performed using either static structures (from e.g. X-ray crystallography), or simulation trajectories, or a mix of the two.
1 Schematic overview of the WatCon Python package. Note that analysis can be performed using either static structures (from e.g. X-ray crystallography), or simulation trajectories, or a mix of the two.CC BY · PubMed Central
2 Visualization of how WatCon differentiates individual water–protein interactions. Two reference points are defined, and the interacting protein atom – water oxygen – reference point angles are measured. The Reference 1 and Reference 2 coordinates are set as using (0, 10, 0) and (10, 0, 10) Å by default (assuming protein structures are aligned to the same coordinate axis), but can also be adjusted to any relevant Cα atom or other coordinate description. In doing so, WatCon can effectively distinguish between (for instance) the interacting water molecules between conformations A and B of the same residue, while also taking into account conserved sequence information. This is useful for analyzing cases where an interacting residue varies within a given family but the interacting water position remains constant.
2 Visualization of how WatCon differentiates individual water–protein interactions. Two reference points are defined, and the interacting protein atom – water oxygen – reference point angles are measured. The Reference 1 and Reference 2 coordinates are set as using (0, 10, 0) and (10, 0, 10) Å by default (assuming protein structures are aligned to the same coordinate axis), but can also be adjusted to any relevant Cα atom or other coordinate description. In doing so, WatCon can effectively distinguish between (for instance) the interacting water molecules between conformations A and B of the same residue, while also taking into account conserved sequence information. This is useful for analyzing cases where an interacting residue varies within a given family but the interacting water position remains constant.CC BY · PubMed Central
3 Comparison of center of mass (COM) distances (Å) between the P-loop and WPD-loop of PTP1B and the calculated number of water–water and water–all (combined water–water and water–protein, denoted Water–Protein) interactions across 8 × 1.5 μs simulation replicas of PTP1B, initiated from each of the WPD-loop closed and open positions (16 trajectories in total). Shown here also are representative structures of the active site water–protein interaction networks in each of the calculated minima on the water–water histogram.
3 Comparison of center of mass (COM) distances (Å) between the P-loop and WPD-loop of PTP1B and the calculated number of water–water and water–all (combined water–water and water–protein, denoted Water–Protein) interactions across 8 × 1.5 μs simulation replicas of PTP1B, initiated from each of the WPD-loop closed and open positions (16 trajectories in total). Shown here also are representative structures of the active site water–protein interaction networks in each of the calculated minima on the water–water histogram.CC BY · PubMed Central
4 (A) Number of water interactions per residue during 8 × 1.5 μs simulations of PTP1B from each of the WPD-loop closed and open conformations (16 trajectories total), normalized by the total number of trajectory frames with key active site residues for PTP1B simulations. Bars are colored by the average number of (nonzero) simultaneous water molecules each residue forms interactions with, to discriminate between, for instance, transient interactions with multiple water molecules simultaneously, vs sustained interactions with a single water molecule. (B) Visualization of residues with a normalized water interaction score > 1. Of the key catalytic loops in PTPs, the WPD-loop is colored blue, the P-loop is colored orange, the E-loop is colored pink, and the Q-loop is colored green.
4 (A) Number of water interactions per residue during 8 × 1.5 μs simulations of PTP1B from each of the WPD-loop closed and open conformations (16 trajectories total), normalized by the total number of trajectory frames with key active site residues for PTP1B simulations. Bars are colored by the average number of (nonzero) simultaneous water molecules each residue forms interactions with, to discriminate between, for instance, transient interactions with multiple water molecules simultaneously, vs sustained interactions with a single water molecule. (B) Visualization of residues with a normalized water interaction score > 1. Of the key catalytic loops in PTPs, the WPD-loop is colored blue, the P-loop is colored orange, the E-loop is colored pink, and the Q-loop is colored green.CC BY · PubMed Central
5 (A–E) Kernel density estimate (KDE) plots of calculated properties, showing a comparison between data obtained from analysis of dynamic trajectories (8 replicas × 1.5 μs simulations of PTP1B initiated from the WPD-loop closed conformation) and of static structures. Shown here are (A) the graph density, (B) graph entropy, (C) the average characteristic path length (CPL) (D) the number of water–water interactions (Water–Water), and (E) the number of water-all interactions (combined water–protein and water–water interactions, denoted Water–Protein). (F) Comparison of highest water occupancy regions obtained from analysis of molecular dynamics trajectories of PTP1B vs clustering on available crystal structures, with the WPD-loop in its catalytically closed conformation. Densities are shown in wire mesh representation, presented at an isovalue of 1.0, calculated from a 9 Å sphere and centered on the center of mass of the R221 and C215 residues, based on 8 × 1.5 μs molecular dynamics simulations of PTP1B. Static structure clusters were calculated using hdbscan clustering based on 82 closed WPD-loop structures of PTP1B (Table S1).
5 (A–E) Kernel density estimate (KDE) plots of calculated properties, showing a comparison between data obtained from analysis of dynamic trajectories (8 replicas × 1.5 μs simulations of PTP1B initiated from the WPD-loop closed conformation) and of static structures. Shown here are (A) the graph density, (B) graph entropy, (C) the average characteristic path length (CPL) (D) the number of water–water interactions (Water–Water), and (E) the number of water-all interactions (combined water–protein and water–water interactions, denoted Water–Protein). (F) Comparison of highest water occupancy regions obtained from analysis of molecular dynamics trajectories of PTP1B vs clustering on available crystal structures, with the WPD-loop in its catalytically closed conformation. Densities are shown in wire mesh representation, presented at an isovalue of 1.0, calculated from a 9 Å sphere and centered on the center of mass of the R221 and C215 residues, based on 8 × 1.5 μs molecular dynamics simulations of PTP1B. Static structure clusters were calculated using hdbscan clustering based on 82 closed WPD-loop structures of PTP1B (Table S1).CC BY · PubMed Central
6 (A) Conservation score to PTP1B closed crystal structure summary network calculated for a set of nonreceptor PTPs using active region waters only. Purple bars correspond to structures with open WPD-loops, and gray hashed bars correspond to structures with closed WPD-loops. (B) Projection of water clusters identified for PTP1B closed crystal structures colored by conservation of particular water positions and by neighbor conservation (blue = less conserved, red = more conserved). WPD-loop is colored blue, and P-loop is colored orange.
6 (A) Conservation score to PTP1B closed crystal structure summary network calculated for a set of nonreceptor PTPs using active region waters only. Purple bars correspond to structures with open WPD-loops, and gray hashed bars correspond to structures with closed WPD-loops. (B) Projection of water clusters identified for PTP1B closed crystal structures colored by conservation of particular water positions and by neighbor conservation (blue = less conserved, red = more conserved). WPD-loop is colored blue, and P-loop is colored orange.CC BY · PubMed Central
7 (A) Calculated protein–water angles for nonreceptor PTPs at D181 (general acid, PTP1B numbering). (B) Calculated protein–water angles for nonreceptor PTPs at Q266 (PTP1B numbering). Backbone interactions are shown in blue and side chain interactions shown in purple. Coordinates associated with open WPD-loop structures are shown as open circles and closed WPD-loop structures with filled circles. Angle 1 was calculated as the angle between the closest interacting protein atom of each residue, the water oxygen, and the Cα atom of residue L71. Angle 2 was calculated as the angle between the interacting protein atom, the water oxygen, and the Cα atom of residue T154.
7 (A) Calculated protein–water angles for nonreceptor PTPs at D181 (general acid, PTP1B numbering). (B) Calculated protein–water angles for nonreceptor PTPs at Q266 (PTP1B numbering). Backbone interactions are shown in blue and side chain interactions shown in purple. Coordinates associated with open WPD-loop structures are shown as open circles and closed WPD-loop structures with filled circles. Angle 1 was calculated as the angle between the closest interacting protein atom of each residue, the water oxygen, and the Cα atom of residue L71. Angle 2 was calculated as the angle between the interacting protein atom, the water oxygen, and the Cα atom of residue T154.CC BY · PubMed Central
8 (A) Wild-type human TPI (PDB ID 2JK2 ) with water clusters shown in transparent spheres colored by conservation score. Structural waters are shown in dark red. WatCon identified a water cluster in TPI that was perfectly conserved between 24 organisms (conservation score = 1.0). This cluster (marked with *) is near the side chain of E105, a residue that causes to TPI deficiency when mutated to aspartate. (B) Identical water clusters shown in A, with E105D mutant TPI (PDB ID 2VOM ) aligned. This mutation causes a visible disruption of the conserved network, as described in prior work. (C) Cartoon representation of the human TPI dimer focused on the active site of chain A. (D) A WatCon calculated water network is shown connecting the side chains of N12, K14, H96, L230, and G233. Water clusters are shown as red spheres with the network connected by black edges. (E) WebLogo sequence alignment highlighting the high conservation of all residues described in (A–D). Residue indexing based on human TPI. Alignment was performed using the MUSCLE web server from EMBL-EBI.
8 (A) Wild-type human TPI (PDB ID 2JK2 ) with water clusters shown in transparent spheres colored by conservation score. Structural waters are shown in dark red. WatCon identified a water cluster in TPI that was perfectly conserved between 24 organisms (conservation score = 1.0). This cluster (marked with *) is near the side chain of E105, a residue that causes to TPI deficiency when mutated to aspartate. (B) Identical water clusters shown in A, with E105D mutant TPI (PDB ID 2VOM ) aligned. This mutation causes a visible disruption of the conserved network, as described in prior work. (C) Cartoon representation of the human TPI dimer focused on the active site of chain A. (D) A WatCon calculated water network is shown connecting the side chains of N12, K14, H96, L230, and G233. Water clusters are shown as red spheres with the network connected by black edges. (E) WebLogo sequence alignment highlighting the high conservation of all residues described in (A–D). Residue indexing based on human TPI. Alignment was performed using the MUSCLE web server from EMBL-EBI.CC BY · PubMed Central
9 (A–C) Projections of water density hotspots obtained from simulations performed on the (A) WT LinB, (B) LinB-OpenW, and (C) LinB-ClosedW structures. Densities are visualized at 1.5σ, and red spheres indicate points of highest density. (D) Calculated interaction scores for catalytic residues D108 and H272. (E) Calculated graph density for each variant. Results were calculated for molecular dynamics trajectories of 3 replicas × 300 ns for each variant.
9 (A–C) Projections of water density hotspots obtained from simulations performed on the (A) WT LinB, (B) LinB-OpenW, and (C) LinB-ClosedW structures. Densities are visualized at 1.5σ, and red spheres indicate points of highest density. (D) Calculated interaction scores for catalytic residues D108 and H272. (E) Calculated graph density for each variant. Results were calculated for molecular dynamics trajectories of 3 replicas × 300 ns for each variant.CC BY · PubMed Central

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Metadata

Authors
Brownless, A.-L. R., Harrison-Rawn, T., & Kamerlin, S. C. L.
Affiliations
Georgia Institute of Technology (US)
Corresponding author
Kamerlin, Shina C. L.
Venue
JACS Au
Published
2025-11-20
Volume
5
Issue
12
Pages
6379-6395
ISSN
2691-3704 (ISSN-L)
OpenAlex
W4416394720
Cited by
2
References
1
Citations by year
2026: 2
FWCI
0.60
Type
journal article
Language
en
Open access
Locations
  • JACS Au (publishedVersion, cc-by)
  • ChemRxiv (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Lund University Publications (Lund University) (submittedVersion)
Funders
  • Vetenskapsrådet (2022-06725)
  • Georgia Research Alliance
  • Vasser Woolley Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords
hydrogen bond network, protein families, graph theory, protein dynamics, protein engineering, pathogenic variants, open-source Python package

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